HEADER ANTIBIOTIC 29-OCT-18 6MW1 TITLE CYCLO-MLE-PHE-MLE-PHE. PSEUDOXYLALLEMYCIN A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOXYLALLEMYCIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: XYLARIA; SOURCE 4 ORGANISM_TAXID: 37991 KEYWDS TETRAPEPTIDE, CYCLIC PEPTIDE, N-METHYL LEUCINE, PSEUDOXYLALLEMYCIN A, KEYWDS 2 ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR A.J.CAMERON,P.W.R.HARRIS,M.A.BRIMBLE,C.J.SQUIRE REVDAT 2 06-NOV-24 6MW1 1 LINK REVDAT 1 11-SEP-19 6MW1 0 JRNL AUTH A.J.CAMERON,C.J.SQUIRE,A.GERENTON,L.A.STUBBING,P.W.R.HARRIS, JRNL AUTH 2 M.A.BRIMBLE JRNL TITL INVESTIGATIONS OF THE KEY MACROLACTAMISATION STEP IN THE JRNL TITL 2 SYNTHESIS OF CYCLIC TETRAPEPTIDE PSEUDOXYLALLEMYCIN A. JRNL REF ORG.BIOMOL.CHEM. V. 17 3902 2019 JRNL REFN ESSN 1477-0539 JRNL PMID 30941386 JRNL DOI 10.1039/C9OB00227H REMARK 2 REMARK 2 RESOLUTION. 0.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : NONE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 40 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FULL LEAST SQUARES REFINEMENT IN SHELXL REMARK 3 WITH ANISOTROPIC ATOMS AND RIDING HYDROGENS. REMARK 4 REMARK 4 6MW1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237718. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.71075 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4124 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.770 REMARK 200 RESOLUTION RANGE LOW (A) : 26.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 11.80 REMARK 200 R MERGE FOR SHELL (I) : 0.14100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 19.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 13.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: METHANOL, WATER, EVAPORATION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 4.81650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.20750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 6.35300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 13.20750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 4.81650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 6.35300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 REMARK 400 THE PSEUDOXYLALLEMYCIN A IS CYCLIC PEPTIDE, A MEMBER OF ANTIBIOTIC REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: PSEUDOXYLALLEMYCIN A REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6MVZ RELATED DB: PDB REMARK 900 LINEAR VERSION OF THIS TETRAPEPTIDE REMARK 900 RELATED ID: 6MW0 RELATED DB: PDB REMARK 900 LINEAR VERSION OF THIS TETRAPEPTIDE WITH TERMINAL D-PHE DBREF 6MW1 A 1001 1004 PDB 6MW1 6MW1 1001 1004 SEQRES 1 A 4 MLE PHE MLE PHE HET MLE A1001 9 HET MLE A1003 9 HETNAM MLE N-METHYLLEUCINE FORMUL 1 MLE 2(C7 H15 N O2) FORMUL 2 HOH *(H2 O) LINK C MLE A1001 N PHE A1002 1555 1555 1.35 LINK N MLE A1001 C PHE A1004 1555 1555 1.37 LINK C PHE A1002 N MLE A1003 1555 1555 1.36 LINK C MLE A1003 N PHE A1004 1555 1555 1.35 CISPEP 1 PHE A 1002 MLE A 1003 0 8.51 CRYST1 9.633 12.706 26.415 90.00 90.00 90.00 P 21 21 21 4 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 0.103810 0.000000 0.000000 0.00000 SCALE2 0.000000 0.078703 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037857 0.00000 HETATM 1 N MLE A1001 0.815 3.319 16.432 1.00 1.10 N ANISOU 1 N MLE A1001 160 125 107 -2 -13 -45 N HETATM 2 CN MLE A1001 0.568 1.887 16.207 1.00 1.72 C ANISOU 2 CN MLE A1001 263 138 214 -37 3 -73 C HETATM 3 CA MLE A1001 1.515 3.711 17.665 1.00 0.94 C ANISOU 3 CA MLE A1001 146 128 62 12 -7 -15 C HETATM 4 CB MLE A1001 0.894 3.081 18.921 1.00 1.25 C ANISOU 4 CB MLE A1001 190 141 114 20 18 31 C HETATM 5 CG MLE A1001 -0.445 3.726 19.321 1.00 1.29 C ANISOU 5 CG MLE A1001 165 185 112 -8 16 44 C HETATM 6 CD1 MLE A1001 -1.182 2.835 20.317 1.00 1.89 C ANISOU 6 CD1 MLE A1001 232 289 156 -63 57 90 C HETATM 7 CD2 MLE A1001 -0.231 5.123 19.925 1.00 1.94 C ANISOU 7 CD2 MLE A1001 308 182 205 40 98 4 C HETATM 8 C MLE A1001 3.047 3.531 17.609 1.00 0.99 C ANISOU 8 C MLE A1001 162 92 97 8 -14 -20 C HETATM 9 O MLE A1001 3.714 3.658 18.628 1.00 1.56 O ANISOU 9 O MLE A1001 180 288 91 30 -21 -35 O ATOM 10 N PHE A1002 3.587 3.362 16.380 1.00 0.88 N ANISOU 10 N PHE A1002 104 136 74 15 -14 -26 N ATOM 11 CA PHE A1002 5.018 3.502 16.131 1.00 0.90 C ANISOU 11 CA PHE A1002 119 118 85 30 0 -31 C ATOM 12 C PHE A1002 5.215 4.568 15.015 1.00 0.95 C ANISOU 12 C PHE A1002 95 150 92 27 -12 -34 C ATOM 13 O PHE A1002 5.692 4.251 13.923 1.00 1.40 O ANISOU 13 O PHE A1002 193 201 105 59 32 -24 O ATOM 14 CB PHE A1002 5.649 2.160 15.706 1.00 1.23 C ANISOU 14 CB PHE A1002 184 139 116 52 22 -32 C ATOM 15 CG PHE A1002 5.337 1.074 16.720 1.00 1.25 C ANISOU 15 CG PHE A1002 196 134 115 73 -5 -34 C ATOM 16 CD1 PHE A1002 6.039 0.994 17.930 1.00 1.72 C ANISOU 16 CD1 PHE A1002 249 188 176 40 -58 -26 C ATOM 17 CD2 PHE A1002 4.296 0.171 16.504 1.00 1.66 C ANISOU 17 CD2 PHE A1002 246 187 160 16 -50 6 C ATOM 18 CE1 PHE A1002 5.711 0.047 18.888 1.00 2.10 C ANISOU 18 CE1 PHE A1002 340 266 146 80 -69 8 C ATOM 19 CE2 PHE A1002 3.960 -0.782 17.469 1.00 2.19 C ANISOU 19 CE2 PHE A1002 303 210 269 -3 -36 33 C ATOM 20 CZ PHE A1002 4.668 -0.839 18.660 1.00 2.04 C ANISOU 20 CZ PHE A1002 327 199 204 87 35 52 C HETATM 21 N MLE A1003 4.781 5.839 15.223 1.00 0.97 N ANISOU 21 N MLE A1003 148 122 77 20 -2 -5 N HETATM 22 CN MLE A1003 4.793 6.715 14.044 1.00 1.44 C ANISOU 22 CN MLE A1003 250 152 113 6 16 22 C HETATM 23 CA MLE A1003 4.283 6.367 16.498 1.00 0.93 C ANISOU 23 CA MLE A1003 144 110 78 13 2 -36 C HETATM 24 CB MLE A1003 4.828 7.770 16.840 1.00 1.20 C ANISOU 24 CB MLE A1003 165 108 157 25 -20 -35 C HETATM 25 CG MLE A1003 6.362 7.905 16.845 1.00 1.36 C ANISOU 25 CG MLE A1003 167 149 171 13 -7 -41 C HETATM 26 CD1 MLE A1003 7.018 6.938 17.818 1.00 2.10 C ANISOU 26 CD1 MLE A1003 177 242 332 17 -82 15 C HETATM 27 CD2 MLE A1003 6.724 9.359 17.198 1.00 1.96 C ANISOU 27 CD2 MLE A1003 197 202 301 -36 -18 -74 C HETATM 28 C MLE A1003 2.738 6.407 16.590 1.00 0.89 C ANISOU 28 C MLE A1003 158 94 65 22 -1 -2 C HETATM 29 O MLE A1003 2.211 6.894 17.585 1.00 1.24 O ANISOU 29 O MLE A1003 173 173 96 34 6 -48 O ATOM 30 N PHE A1004 2.052 5.832 15.583 1.00 0.97 N ANISOU 30 N PHE A1004 128 150 68 50 -7 -24 N ATOM 31 CA PHE A1004 0.596 5.692 15.629 1.00 1.05 C ANISOU 31 CA PHE A1004 129 165 81 30 -19 -13 C ATOM 32 C PHE A1004 0.205 4.192 15.577 1.00 1.20 C ANISOU 32 C PHE A1004 125 206 96 25 -10 -55 C ATOM 33 O PHE A1004 -0.607 3.804 14.734 1.00 2.00 O ANISOU 33 O PHE A1004 200 300 214 -25 -98 -82 O ATOM 34 CB PHE A1004 -0.056 6.463 14.461 1.00 1.52 C ANISOU 34 CB PHE A1004 155 278 109 59 -49 -1 C ATOM 35 CG PHE A1004 0.594 7.820 14.297 1.00 1.63 C ANISOU 35 CG PHE A1004 206 229 146 67 -72 38 C ATOM 36 CD1 PHE A1004 0.503 8.781 15.309 1.00 2.21 C ANISOU 36 CD1 PHE A1004 330 265 195 49 -63 9 C ATOM 37 CD2 PHE A1004 1.403 8.098 13.196 1.00 2.55 C ANISOU 37 CD2 PHE A1004 361 335 215 98 20 109 C ATOM 38 CE1 PHE A1004 1.241 9.961 15.230 1.00 3.31 C ANISOU 38 CE1 PHE A1004 572 249 361 -9 -220 23 C ATOM 39 CE2 PHE A1004 2.146 9.276 13.125 1.00 3.62 C ANISOU 39 CE2 PHE A1004 441 452 401 27 26 290 C ATOM 40 CZ PHE A1004 2.085 10.196 14.152 1.00 3.75 C ANISOU 40 CZ PHE A1004 498 312 528 -70 -246 245 C TER 41 PHE A1004 HETATM 42 O HOH A2001 7.494 2.549 12.771 1.00 1.49 O ANISOU 42 O HOH A2001 138 270 126 -1 7 -106 O CONECT 1 2 3 32 CONECT 2 1 CONECT 3 1 4 8 CONECT 4 3 5 CONECT 5 4 6 7 CONECT 6 5 CONECT 7 5 CONECT 8 3 9 10 CONECT 9 8 CONECT 10 8 CONECT 12 21 CONECT 21 12 22 23 CONECT 22 21 CONECT 23 21 24 28 CONECT 24 23 25 CONECT 25 24 26 27 CONECT 26 25 CONECT 27 25 CONECT 28 23 29 30 CONECT 29 28 CONECT 30 28 CONECT 32 1 MASTER 198 0 2 0 0 0 0 6 41 1 22 1 END