HEADER ANTIBIOTIC 29-OCT-18 6MW2 TITLE CYCLO-MLE-PHE-MLE-D-PHE. D-PHE ANALOGUE OF 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, ANALOGUE OF KEYWDS 2 PSEUDOXYLALLEMYCIN A, ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR A.J.CAMERON,P.W.R.HARRIS,M.A.BRIMBLE,C.J.SQUIRE REVDAT 3 23-OCT-24 6MW2 1 LINK REVDAT 2 02-OCT-19 6MW2 1 REMARK REVDAT 1 11-SEP-19 6MW2 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) : 20.49 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 : 0 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 ATOMIC DISPLACEMENT PARAMETERS AND RIDING REMARK 3 HYDROGENS. REMARK 4 REMARK 4 6MW2 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_1000237719. 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 : 3920 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.770 REMARK 200 RESOLUTION RANGE LOW (A) : 20.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.1000 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 (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.09300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 19.10 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 (%): 8.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: METHANOL, ETHANOL, TETRAHYDROFURAN, REMARK 280 WATER, EVAPORATION, 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 5.46400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 10.24400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 6.77600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 10.24400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 5.46400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 6.77600 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: 750 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 CYCLO-MLE-PHE-MLE-D-PHE. D-PHE ANALOGUE OF PSEUDOXYLALLEMYCIN A REMARK 400 IS CYCLIC PEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: CYCLO-MLE-PHE-MLE-D-PHE. D-PHE ANALOGUE OF REMARK 400 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 TETRAPETIDE OF PSEUDOXYLALLEMYCIN A REMARK 900 RELATED ID: 6MW0 RELATED DB: PDB REMARK 900 LINEAR TETRAPEPTIDE RELATED TO PSEUDOXYLALLEMYCIN A REMARK 900 RELATED ID: 6MW1 RELATED DB: PDB REMARK 900 PSEUDOXYLALLEMYCIN A DBREF 6MW2 A 1001 1004 PDB 6MW2 6MW2 1001 1004 SEQRES 1 A 4 MLE PHE MLE DPN HET MLE A1001 9 HET MLE A1003 9 HET DPN A1004 11 HETNAM MLE N-METHYLLEUCINE HETNAM DPN D-PHENYLALANINE FORMUL 1 MLE 2(C7 H15 N O2) FORMUL 1 DPN C9 H11 N O2 LINK C MLE A1001 N PHE A1002 1555 1555 1.36 LINK N MLE A1001 C DPN A1004 1555 1555 1.37 LINK C PHE A1002 N MLE A1003 1555 1555 1.36 LINK C MLE A1003 N DPN A1004 1555 1555 1.35 CISPEP 1 PHE A 1002 MLE A 1003 0 -11.70 CRYST1 10.928 13.552 20.488 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 0.091508 0.000000 0.000000 0.00000 SCALE2 0.000000 0.073790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.048809 0.00000 HETATM 1 N MLE A1001 4.901 11.429 8.558 1.00 1.54 N ANISOU 1 N MLE A1001 158 202 192 -14 4 3 N HETATM 2 CN MLE A1001 5.724 12.032 7.498 1.00 1.85 C ANISOU 2 CN MLE A1001 190 242 229 -7 44 21 C HETATM 3 CA MLE A1001 3.451 11.301 8.346 1.00 1.49 C ANISOU 3 CA MLE A1001 141 197 195 10 4 12 C HETATM 4 CB MLE A1001 2.781 12.546 7.721 1.00 1.74 C ANISOU 4 CB MLE A1001 198 207 216 30 -23 16 C HETATM 5 CG MLE A1001 2.537 13.715 8.694 1.00 1.99 C ANISOU 5 CG MLE A1001 238 209 264 52 17 -5 C HETATM 6 CD1 MLE A1001 1.539 14.679 8.051 1.00 2.67 C ANISOU 6 CD1 MLE A1001 319 287 350 111 19 35 C HETATM 7 CD2 MLE A1001 3.811 14.470 9.081 1.00 3.22 C ANISOU 7 CD2 MLE A1001 328 280 542 45 -107 -121 C HETATM 8 C MLE A1001 3.045 10.034 7.563 1.00 1.50 C ANISOU 8 C MLE A1001 166 205 166 4 -7 23 C HETATM 9 O MLE A1001 1.854 9.755 7.445 1.00 1.81 O ANISOU 9 O MLE A1001 141 256 250 6 10 -29 O ATOM 10 N PHE A1002 4.035 9.239 7.077 1.00 1.48 N ANISOU 10 N PHE A1002 135 193 203 3 7 0 N ATOM 11 CA PHE A1002 3.715 7.989 6.384 1.00 1.50 C ANISOU 11 CA PHE A1002 153 206 177 -2 -9 -4 C ATOM 12 C PHE A1002 4.676 6.876 6.827 1.00 1.56 C ANISOU 12 C PHE A1002 184 172 202 -5 -3 -22 C ATOM 13 O PHE A1002 5.459 6.375 6.009 1.00 2.10 O ANISOU 13 O PHE A1002 254 274 221 81 30 -21 O ATOM 14 CB PHE A1002 3.734 8.158 4.848 1.00 1.83 C ANISOU 14 CB PHE A1002 227 251 176 20 -21 -15 C ATOM 15 CG PHE A1002 2.856 9.303 4.415 1.00 1.77 C ANISOU 15 CG PHE A1002 206 284 141 5 -5 0 C ATOM 16 CD1 PHE A1002 1.492 9.098 4.137 1.00 2.10 C ANISOU 16 CD1 PHE A1002 221 243 286 -38 -59 -14 C ATOM 17 CD2 PHE A1002 3.357 10.601 4.345 1.00 1.84 C ANISOU 17 CD2 PHE A1002 170 288 200 -36 -11 43 C ATOM 18 CE1 PHE A1002 0.672 10.180 3.819 1.00 2.53 C ANISOU 18 CE1 PHE A1002 223 332 350 -6 -71 5 C ATOM 19 CE2 PHE A1002 2.539 11.677 4.044 1.00 2.09 C ANISOU 19 CE2 PHE A1002 248 279 221 -33 -13 40 C ATOM 20 CZ PHE A1002 1.189 11.470 3.778 1.00 2.31 C ANISOU 20 CZ PHE A1002 219 308 298 41 -48 20 C HETATM 21 N MLE A1003 4.623 6.440 8.118 1.00 1.64 N ANISOU 21 N MLE A1003 194 178 214 42 17 6 N HETATM 22 CN MLE A1003 5.660 5.483 8.511 1.00 1.99 C ANISOU 22 CN MLE A1003 235 235 242 74 7 10 C HETATM 23 CA MLE A1003 3.873 7.144 9.170 1.00 1.48 C ANISOU 23 CA MLE A1003 162 172 195 18 22 -10 C HETATM 24 CB MLE A1003 3.393 6.219 10.301 1.00 1.65 C ANISOU 24 CB MLE A1003 199 198 190 -4 -1 5 C HETATM 25 CG MLE A1003 2.587 5.001 9.819 1.00 1.89 C ANISOU 25 CG MLE A1003 267 182 226 -29 29 5 C HETATM 26 CD1 MLE A1003 2.111 4.199 11.032 1.00 2.73 C ANISOU 26 CD1 MLE A1003 437 268 271 -117 33 33 C HETATM 27 CD2 MLE A1003 1.401 5.417 8.938 1.00 2.46 C ANISOU 27 CD2 MLE A1003 294 284 301 -74 -61 8 C HETATM 28 C MLE A1003 4.744 8.295 9.723 1.00 1.48 C ANISOU 28 C MLE A1003 158 178 191 32 0 28 C HETATM 29 O MLE A1003 5.958 8.348 9.523 1.00 1.88 O ANISOU 29 O MLE A1003 146 246 279 3 28 -18 O HETATM 30 N DPN A1004 4.082 9.254 10.411 1.00 1.37 N ANISOU 30 N DPN A1004 118 171 202 -1 -3 -5 N HETATM 31 CA DPN A1004 4.829 10.414 10.890 1.00 1.47 C ANISOU 31 CA DPN A1004 153 196 175 -11 -14 -3 C HETATM 32 C DPN A1004 5.524 11.198 9.751 1.00 1.51 C ANISOU 32 C DPN A1004 143 185 212 10 10 0 C HETATM 33 O DPN A1004 6.682 11.591 9.936 1.00 1.86 O ANISOU 33 O DPN A1004 139 263 264 -16 -13 -4 O HETATM 34 CB DPN A1004 3.972 11.322 11.785 1.00 1.83 C ANISOU 34 CB DPN A1004 241 208 204 4 14 -1 C HETATM 35 CG DPN A1004 3.473 10.684 13.076 1.00 1.79 C ANISOU 35 CG DPN A1004 184 245 210 -51 -26 -46 C HETATM 36 CD1 DPN A1004 2.469 11.358 13.789 1.00 2.10 C ANISOU 36 CD1 DPN A1004 215 275 261 -7 12 -48 C HETATM 37 CD2 DPN A1004 3.986 9.499 13.607 1.00 2.13 C ANISOU 37 CD2 DPN A1004 230 292 238 -5 -7 5 C HETATM 38 CE1 DPN A1004 2.013 10.867 15.008 1.00 2.59 C ANISOU 38 CE1 DPN A1004 230 431 263 -35 51 -66 C HETATM 39 CE2 DPN A1004 3.496 8.996 14.818 1.00 2.50 C ANISOU 39 CE2 DPN A1004 268 379 248 -44 -46 49 C HETATM 40 CZ DPN A1004 2.517 9.673 15.524 1.00 2.73 C ANISOU 40 CZ DPN A1004 255 495 225 -127 22 25 C TER 41 DPN A1004 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 31 CONECT 31 30 32 34 CONECT 32 1 31 33 CONECT 33 32 CONECT 34 31 35 CONECT 35 34 36 37 CONECT 36 35 38 CONECT 37 35 39 CONECT 38 36 40 CONECT 39 37 40 CONECT 40 38 39 MASTER 202 0 3 0 0 0 0 6 40 1 31 1 END