HEADER ANTIBIOTIC 30-OCT-18 6MXF TITLE MICROED STRUCTURE OF THIOSTREPTON AT 1.9 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOSTREPTON; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOMYCES AZUREUS; SOURCE 4 ORGANISM_TAXID: 146537 KEYWDS ANTIBIOTIC EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR C.G.JONES,M.W.MARTYNOWYCZ,J.HATTNE,T.FULTON,B.M.STOLTZ,J.A.RODRIGUEZ, AUTHOR 2 H.M.NELSON,T.GONEN REVDAT 6 15-NOV-23 6MXF 1 LINK REVDAT 5 11-OCT-23 6MXF 1 REMARK LINK REVDAT 4 27-NOV-19 6MXF 1 SEQRES REVDAT 3 06-FEB-19 6MXF 1 DBREF REVDAT 2 02-JAN-19 6MXF 1 JRNL REMARK SITE REVDAT 1 21-NOV-18 6MXF 0 JRNL AUTH C.G.JONES,M.W.MARTYNOWYCZ,J.HATTNE,T.J.FULTON,B.M.STOLTZ, JRNL AUTH 2 J.A.RODRIGUEZ,H.M.NELSON,T.GONEN JRNL TITL THE CRYOEM METHOD MICROED AS A POWERFUL TOOL FOR SMALL JRNL TITL 2 MOLECULE STRUCTURE DETERMINATION. JRNL REF ACS CENT SCI V. 4 1587 2018 JRNL REFN ESSN 2374-7943 JRNL PMID 30555912 JRNL DOI 10.1021/ACSCENTSCI.8B00760 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 78.2 REMARK 3 NUMBER OF REFLECTIONS : 620 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.400 REMARK 3 FREE R VALUE TEST SET COUNT : 57 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 3.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.1820 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : 0.0000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 114 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 6.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : 0.18000 REMARK 3 B33 (A**2) : -0.37000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.352 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.202 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.282 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 123 ; 0.015 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 107 ; 0.025 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 120 ; 2.760 ; 2.241 REMARK 3 BOND ANGLES OTHERS (DEGREES): 213 ; 1.374 ; 2.283 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 3 ; 3.623 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 4 ; 7.901 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 15 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 135 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 49 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 62 ; 0.625 ; 0.798 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 63 ; 0.620 ; 0.810 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 37 ; 0.893 ; 1.194 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 38 ; 0.881 ; 1.223 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 60 ; 0.609 ; 0.743 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 61 ; 0.604 ; 0.754 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 84 ; 0.892 ; 1.161 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 101 ; 1.546 ;10.960 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 102 ; 1.539 ;10.959 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6MXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237739. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : 03-OCT-18 REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 240 DETECTOR TYPE : FEI CETA (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 686 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 240 RESOLUTION RANGE LOW (A) : 18.990 REMARK 240 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 240 COMPLETENESS FOR RANGE (%) : 78.6 REMARK 240 DATA REDUNDANCY : 8.100 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.90 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :2.13 REMARK 240 COMPLETENESS FOR SHELL (%) : 40.3 REMARK 240 DATA REDUNDANCY IN SHELL : 4.90 REMARK 240 R MERGE FOR SHELL (I) : 0.32000 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : MOLREP 11.6.04 REMARK 240 STARTING MODEL : 1E9W REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.76700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 13.10950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 13.10950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.65050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 13.10950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 13.10950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 6.88350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 13.10950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 13.10950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.65050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 13.10950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 13.10950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 6.88350 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 13.76700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES REMARK 400 CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A REMARK 400 NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO REMARK 400 ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING REMARK 400 THIAZOLES, THIAZOLINES AND OXAZOLES. REMARK 400 HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES) REMARK 400 REMARK 400 THE THIOSTREPTON IS THIOPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: THIOSTREPTON REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: Thiostrepton is a hetrocyclic thiopeptide belonging REMARK 400 to the thiocillin family, consisting of four REMARK 400 thiazole, one thiozoline and one piperideine rings. REMARK 400 A modified quinoline linked to main-chain residue 1 REMARK 400 and side-chain of residue 12. Post translational REMARK 400 maturation of thiazole and oxazole containing REMARK 400 antibiotics involves the enzymic condensation of a REMARK 400 Cys or Ser with the alpha-carbonyl of the preceding REMARK 400 amino acid to form a thioether or ether bond, then REMARK 400 dehydration to form a double bond with the alpha- REMARK 400 amino nitrogen. Thiazoline or oxazoline ring are REMARK 400 dehydrogenated to form thiazole or oxazole rings. REMARK 400 the pyridinyl involves the cross-linking of a Ser REMARK 400 and a Cys-Ser pair usually separated by 7 or 8 REMARK 400 residues along the peptide chain. The Ser residues REMARK 400 are dehydrated to didehydroalanines, then bonded REMARK 400 between their beta carbons. The alpha carbonyl of REMARK 400 the Cys condenses with alpha carbon of the first Ser REMARK 400 to form a pyridinyl ring. The ring may be mutiply REMARK 400 dehydrogenated to form a pyridine ring with loss of REMARK 400 the amino nitrogen of the first Ser. The amidation REMARK 400 of Ser-17 probably does not occur by the same REMARK 400 mechanism, oxidative cleavage of glycine, as in REMARK 400 eukaryotes. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O12 QUA A 0 OG1 THR A 12 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DHA A 16 C - N - CA ANGL. DEV. = 23.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 5 77.93 63.70 REMARK 500 DCY A 9 -2.00 -135.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 BB9 A 13 MH6 A 14 145.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 BB9 A 6 14.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for THIOSTREPTON chain A REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-9292 RELATED DB: EMDB REMARK 900 MICROED STRUCTURE OF THIOSTREPTON AT 1.9 A RESOLUTION REMARK 900 RELATED ID: EMD-9291 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9290 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9282 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9283 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9284 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9285 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9286 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9287 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9288 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9289 RELATED DB: EMDB DBREF 6MXF A 0 18 PDB 6MXF 6MXF 0 18 SEQRES 1 A 19 QUA ILE ALA DHA ALA SER BB9 THR DBU DCY TS9 BB9 THR SEQRES 2 A 19 BB9 MH6 BB9 DHA DHA NH2 HET QUA A 0 16 HET DHA A 3 5 HET BB9 A 6 6 HET DBU A 8 5 HET DCY A 9 6 HET TS9 A 10 9 HET BB9 A 11 6 HET BB9 A 13 5 HET MH6 A 14 4 HET BB9 A 15 6 HET DHA A 16 5 HET DHA A 17 5 HET NH2 A 18 1 HETNAM QUA 8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID HETNAM DHA 2-AMINO-ACRYLIC ACID HETNAM BB9 (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID HETNAM DBU (2Z)-2-AMINOBUT-2-ENOIC ACID HETNAM DCY D-CYSTEINE HETNAM TS9 (2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC ACID HETNAM MH6 3-HYDROXY-2-IMINOPROPANOIC ACID HETNAM NH2 AMINO GROUP HETSYN DHA 2,3-DIDEHYDROALANINE HETSYN DBU Z-DEHYDROBUTYRINE FORMUL 1 QUA C12 H13 N O4 FORMUL 1 DHA 3(C3 H5 N O2) FORMUL 1 BB9 4(C3 H5 N O2 S) FORMUL 1 DBU C4 H7 N O2 FORMUL 1 DCY C3 H7 N O2 S FORMUL 1 TS9 C6 H13 N O4 FORMUL 1 MH6 C3 H5 N O3 FORMUL 1 NH2 H2 N FORMUL 2 HOH *2(H2 O) LINK C7 QUA A 0 N ILE A 1 1555 1555 1.55 LINK C11 QUA A 0 OG1 THR A 12 1555 1555 1.31 LINK C ALA A 2 N DHA A 3 1555 1555 1.35 LINK C DHA A 3 N ALA A 4 1555 1555 1.42 LINK C SER A 5 N BB9 A 6 1555 1555 1.34 LINK C SER A 5 SG BB9 A 6 1555 1555 1.72 LINK CA SER A 5 C BB9 A 13 1555 1555 1.51 LINK CB SER A 5 CB MH6 A 14 1555 1555 1.58 LINK C BB9 A 6 N THR A 7 1555 1555 1.42 LINK C THR A 7 N DBU A 8 1555 1555 1.36 LINK C DBU A 8 SG DCY A 9 1555 1555 1.72 LINK C DBU A 8 N DCY A 9 1555 1555 1.41 LINK C DCY A 9 N TS9 A 10 1555 1555 1.35 LINK C TS9 A 10 SG BB9 A 11 1555 1555 1.71 LINK C TS9 A 10 N BB9 A 11 1555 1555 1.33 LINK C BB9 A 11 N THR A 12 1555 1555 1.39 LINK C THR A 12 SG BB9 A 13 1555 1555 1.71 LINK C THR A 12 N BB9 A 13 1555 1555 1.33 LINK C BB9 A 13 N MH6 A 14 1555 1555 1.38 LINK C MH6 A 14 N BB9 A 15 1555 1555 1.34 LINK C MH6 A 14 SG BB9 A 15 1555 1555 1.68 LINK C BB9 A 15 N DHA A 16 1555 1555 1.34 LINK C DHA A 16 N DHA A 17 1555 1555 1.39 LINK C DHA A 17 N NH2 A 18 1555 1555 1.28 SITE 1 AC1 2 HOH A 101 HOH A 102 CRYST1 26.219 26.219 27.534 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.038140 0.000000 0.000000 0.00000 SCALE2 0.000000 0.038140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036319 0.00000 HETATM 1 O12 QUA A 0 10.846 5.950 -3.568 1.00 5.38 O HETATM 2 C11 QUA A 0 9.756 5.430 -3.418 1.00 5.55 C HETATM 3 C2 QUA A 0 9.569 3.950 -3.605 1.00 6.27 C HETATM 4 N1 QUA A 0 8.323 3.479 -3.469 1.00 6.37 N HETATM 5 C3 QUA A 0 10.644 3.163 -3.979 1.00 6.46 C HETATM 6 C9 QUA A 0 8.090 2.191 -3.746 1.00 6.39 C HETATM 7 C4 QUA A 0 10.418 1.813 -4.212 1.00 6.67 C HETATM 8 C8 QUA A 0 6.630 1.779 -3.753 1.00 6.46 C HETATM 9 C10 QUA A 0 9.113 1.302 -4.110 1.00 6.56 C HETATM 10 O16 QUA A 0 6.068 1.903 -5.062 1.00 6.25 O HETATM 11 C7 QUA A 0 6.526 0.325 -3.301 1.00 6.74 C HETATM 12 C13 QUA A 0 11.569 0.863 -4.484 1.00 6.78 C HETATM 13 O15 QUA A 0 12.634 1.475 -5.206 1.00 7.06 O HETATM 14 C5 QUA A 0 8.784 -0.089 -4.285 1.00 6.50 C HETATM 15 C14 QUA A 0 12.092 0.266 -3.210 1.00 6.98 C HETATM 16 C6 QUA A 0 7.570 -0.536 -3.956 1.00 6.51 C ATOM 17 N ILE A 1 6.536 -0.046 -1.799 1.00 7.73 N ATOM 18 CA ILE A 1 5.563 0.737 -0.968 1.00 7.86 C ATOM 19 C ILE A 1 6.255 1.917 -0.265 1.00 7.83 C ATOM 20 O ILE A 1 5.548 2.757 0.275 1.00 7.34 O ATOM 21 CB ILE A 1 4.846 -0.166 0.056 1.00 8.34 C ATOM 22 CG1 ILE A 1 5.850 -0.751 1.058 1.00 8.54 C ATOM 23 CG2 ILE A 1 4.004 -1.220 -0.650 1.00 8.28 C ATOM 24 CD1 ILE A 1 5.230 -1.487 2.230 1.00 8.80 C ATOM 25 N ALA A 2 7.586 1.945 -0.214 1.00 7.97 N ATOM 26 CA ALA A 2 8.348 3.093 0.318 1.00 8.02 C ATOM 27 C ALA A 2 9.792 3.023 -0.191 1.00 7.48 C ATOM 28 O ALA A 2 10.206 1.927 -0.550 1.00 7.19 O ATOM 29 CB ALA A 2 8.293 3.122 1.823 1.00 8.08 C HETATM 30 N DHA A 3 10.440 4.201 -0.080 1.00 6.39 N HETATM 31 CA DHA A 3 11.606 4.576 -0.640 1.00 6.07 C HETATM 32 CB DHA A 3 12.572 3.701 -0.913 1.00 5.81 C HETATM 33 C DHA A 3 11.707 6.012 -0.922 1.00 5.70 C HETATM 34 O DHA A 3 10.688 6.662 -0.582 1.00 5.67 O ATOM 35 N ALA A 4 12.950 6.615 -1.269 1.00 5.17 N ATOM 36 CA ALA A 4 13.040 7.928 -1.954 1.00 5.05 C ATOM 37 C ALA A 4 13.658 7.730 -3.347 1.00 5.05 C ATOM 38 O ALA A 4 14.744 7.150 -3.427 1.00 4.98 O ATOM 39 CB ALA A 4 13.860 8.885 -1.122 1.00 5.08 C ATOM 40 N SER A 5 13.019 8.291 -4.380 1.00 5.06 N ATOM 41 CA SER A 5 13.428 8.204 -5.807 1.00 5.18 C ATOM 42 C SER A 5 13.368 6.747 -6.304 1.00 5.10 C ATOM 43 CB SER A 5 14.812 8.807 -5.984 1.00 5.63 C HETATM 44 N BB9 A 6 12.292 6.028 -6.664 1.00 4.98 N HETATM 45 CA BB9 A 6 12.535 4.769 -7.023 1.00 5.01 C HETATM 46 C BB9 A 6 11.542 3.868 -7.573 1.00 4.99 C HETATM 47 O BB9 A 6 11.628 2.663 -7.295 1.00 4.90 O HETATM 48 CB BB9 A 6 13.785 4.396 -6.782 1.00 5.16 C HETATM 49 SG BB9 A 6 14.688 5.664 -6.084 1.00 5.00 S ATOM 50 N THR A 7 10.301 4.501 -7.857 1.00 5.32 N ATOM 51 CA THR A 7 9.102 3.767 -8.259 1.00 5.40 C ATOM 52 C THR A 7 8.444 4.551 -9.398 1.00 5.72 C ATOM 53 O THR A 7 8.763 5.760 -9.558 1.00 5.34 O ATOM 54 CB THR A 7 8.206 3.517 -7.033 1.00 5.43 C ATOM 55 OG1 THR A 7 7.218 2.536 -7.355 1.00 5.43 O ATOM 56 CG2 THR A 7 7.506 4.766 -6.534 1.00 5.56 C HETATM 57 N DBU A 8 7.345 4.161 -10.090 1.00 6.64 N HETATM 58 CA DBU A 8 6.567 4.862 -10.920 1.00 6.72 C HETATM 59 CB DBU A 8 7.054 5.379 -12.070 1.00 7.02 C HETATM 60 CG DBU A 8 8.490 5.160 -12.530 1.00 7.08 C HETATM 61 C DBU A 8 5.153 5.100 -10.618 1.00 7.34 C HETATM 62 N DCY A 9 4.604 4.402 -9.518 1.00 8.16 N HETATM 63 CA DCY A 9 3.163 4.403 -9.614 1.00 8.49 C HETATM 64 C DCY A 9 2.485 4.728 -8.275 1.00 9.26 C HETATM 65 O DCY A 9 1.240 4.758 -8.286 1.00 9.42 O HETATM 66 CB DCY A 9 2.775 5.393 -10.698 1.00 8.31 C HETATM 67 SG DCY A 9 4.103 5.543 -11.905 1.00 7.60 S HETATM 68 N TS9 A 10 3.231 4.932 -7.175 1.00 9.21 N HETATM 69 CA TS9 A 10 2.644 5.261 -5.845 1.00 9.94 C HETATM 70 C TS9 A 10 3.047 6.676 -5.398 1.00 8.20 C HETATM 71 CB TS9 A 10 2.939 4.176 -4.798 1.00 10.91 C HETATM 72 OG3 TS9 A 10 4.363 4.010 -4.756 1.00 11.48 O HETATM 73 CG2 TS9 A 10 2.489 4.637 -3.413 1.00 11.34 C HETATM 74 CG1 TS9 A 10 2.251 2.864 -5.257 1.00 12.21 C HETATM 75 OD2 TS9 A 10 0.827 3.035 -5.400 1.00 12.20 O HETATM 76 CD1 TS9 A 10 2.500 1.710 -4.306 1.00 12.61 C HETATM 77 N BB9 A 11 4.312 7.001 -5.147 1.00 6.87 N HETATM 78 CA BB9 A 11 4.502 8.323 -5.118 1.00 6.56 C HETATM 79 C BB9 A 11 5.814 8.913 -4.817 1.00 5.98 C HETATM 80 O BB9 A 11 6.055 10.127 -4.989 1.00 6.29 O HETATM 81 CB BB9 A 11 3.403 9.032 -5.430 1.00 6.52 C HETATM 82 SG BB9 A 11 2.070 8.044 -5.706 1.00 6.50 S ATOM 83 N THR A 12 6.872 8.037 -4.580 1.00 5.28 N ATOM 84 CA THR A 12 8.243 8.480 -4.163 1.00 4.99 C ATOM 85 C THR A 12 9.150 8.418 -5.392 1.00 4.75 C ATOM 86 CB THR A 12 8.735 7.628 -2.997 1.00 5.05 C ATOM 87 OG1 THR A 12 8.745 6.259 -3.416 1.00 5.11 O ATOM 88 CG2 THR A 12 7.869 7.776 -1.759 1.00 5.19 C HETATM 89 N BB9 A 13 10.438 8.693 -5.242 1.00 4.68 N HETATM 90 CA BB9 A 13 11.025 8.757 -6.413 1.00 4.73 C HETATM 91 C BB9 A 13 12.462 9.086 -6.566 1.00 5.14 C HETATM 92 CB BB9 A 13 10.179 8.514 -7.428 1.00 4.65 C HETATM 93 SG BB9 A 13 8.570 8.233 -6.992 1.00 4.36 S HETATM 94 N MH6 A 14 12.677 10.395 -6.191 1.00 5.74 N HETATM 95 CA MH6 A 14 13.704 10.877 -5.607 1.00 5.72 C HETATM 96 C MH6 A 14 13.803 12.303 -5.171 1.00 9.27 C HETATM 97 CB MH6 A 14 15.011 10.219 -5.309 1.00 5.95 C HETATM 98 N BB9 A 15 14.625 12.665 -4.176 1.00 11.23 N HETATM 99 CA BB9 A 15 14.458 13.946 -3.941 1.00 11.87 C HETATM 100 C BB9 A 15 15.449 14.750 -3.201 1.00 12.66 C HETATM 101 O BB9 A 15 15.078 15.904 -2.867 1.00 13.48 O HETATM 102 CB BB9 A 15 13.347 14.425 -4.459 1.00 11.78 C HETATM 103 SG BB9 A 15 12.434 13.267 -5.281 1.00 11.74 S HETATM 104 N DHA A 16 16.710 14.367 -2.976 1.00 14.44 N HETATM 105 CA DHA A 16 17.908 14.746 -2.561 1.00 15.77 C HETATM 106 CB DHA A 16 17.955 15.671 -1.613 1.00 18.20 C HETATM 107 C DHA A 16 19.124 14.169 -3.134 1.00 16.09 C HETATM 108 O DHA A 16 19.041 13.635 -4.287 1.00 15.91 O HETATM 109 N DHA A 17 20.286 14.114 -2.382 1.00 15.70 N HETATM 110 CA DHA A 17 21.522 13.704 -2.713 1.00 15.41 C HETATM 111 CB DHA A 17 21.709 12.667 -3.524 1.00 15.59 C HETATM 112 C DHA A 17 22.719 14.354 -2.172 1.00 14.77 C HETATM 113 O DHA A 17 22.595 14.984 -1.101 1.00 14.89 O HETATM 114 N NH2 A 18 23.856 14.504 -2.745 1.00 14.10 N TER 115 NH2 A 18 HETATM 116 O HOH A 101 5.403 5.113 0.255 0.50 4.25 O HETATM 117 O HOH A 102 5.975 5.285 -2.864 1.00 12.00 O CONECT 1 2 CONECT 2 1 3 87 CONECT 3 2 4 5 CONECT 4 3 6 CONECT 5 3 7 CONECT 6 4 8 9 CONECT 7 5 9 12 CONECT 8 6 10 11 CONECT 9 6 7 14 CONECT 10 8 CONECT 11 8 16 17 CONECT 12 7 13 15 CONECT 13 12 CONECT 14 9 16 CONECT 15 12 CONECT 16 11 14 CONECT 17 11 CONECT 27 30 CONECT 30 27 31 CONECT 31 30 32 33 CONECT 32 31 CONECT 33 31 34 35 CONECT 34 33 CONECT 35 33 CONECT 41 91 CONECT 42 44 49 CONECT 43 97 CONECT 44 42 45 CONECT 45 44 46 48 CONECT 46 45 47 50 CONECT 47 46 CONECT 48 45 49 CONECT 49 42 48 CONECT 50 46 CONECT 52 57 CONECT 57 52 58 CONECT 58 57 59 61 CONECT 59 58 60 CONECT 60 59 CONECT 61 58 62 67 CONECT 62 61 63 CONECT 63 62 64 66 CONECT 64 63 65 68 CONECT 65 64 CONECT 66 63 67 CONECT 67 61 66 CONECT 68 64 69 CONECT 69 68 70 71 CONECT 70 69 77 82 CONECT 71 69 72 73 74 CONECT 72 71 CONECT 73 71 CONECT 74 71 75 76 CONECT 75 74 CONECT 76 74 CONECT 77 70 78 CONECT 78 77 79 81 CONECT 79 78 80 83 CONECT 80 79 CONECT 81 78 82 CONECT 82 70 81 CONECT 83 79 CONECT 85 89 93 CONECT 87 2 CONECT 89 85 90 CONECT 90 89 91 92 CONECT 91 41 90 94 CONECT 92 90 93 CONECT 93 85 92 CONECT 94 91 95 CONECT 95 94 96 97 CONECT 96 95 98 103 CONECT 97 43 95 CONECT 98 96 99 CONECT 99 98 100 102 CONECT 100 99 101 104 CONECT 101 100 CONECT 102 99 103 CONECT 103 96 102 CONECT 104 100 105 CONECT 105 104 106 107 CONECT 106 105 CONECT 107 105 108 109 CONECT 108 107 CONECT 109 107 110 CONECT 110 109 111 112 CONECT 111 110 CONECT 112 110 113 114 CONECT 113 112 CONECT 114 112 MASTER 359 0 13 0 0 0 1 6 116 1 90 2 END