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