HEADER HYDROLASE 23-SEP-13 4MUQ TITLE CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE VANXYG IN TITLE 2 COMPLEX WITH D-ALA-D-ALA PHOSPHINATE ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: D,D-DIPEPTIDASE/D,D-CARBOXYPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VANXYG; COMPND 5 SYNONYM: D,D-PEPTIDASE, VANXYG; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_TAXID: 1351; SOURCE 4 STRAIN: BM4518; SOURCE 5 GENE: VANXYG, VANYG2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P15-TC LIC KEYWDS CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, KEYWDS 2 NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, NIAID, KEYWDS 3 ALPHA+BETA PROTEIN, METALLOPEPTIDASE, HEDGEHOG/DD-PEPTIDASE FOLD, KEYWDS 4 MEROPS M15B SUBFAMILY, ZN2+-DEPENDENT D, D-DIPEPTIDASE, VANCOMYCIN KEYWDS 5 RESISTANCE, ANTIBIOTIC RESISTANCE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.J.STOGIOS,E.EVDOKIMOVA,D.MEZIANE-CHERIF,R.DI LEO,V.YIM,P.COURVALIN, AUTHOR 2 A.SAVCHENKO,W.F.ANDERSON,CENTER FOR STRUCTURAL GENOMICS OF AUTHOR 3 INFECTIOUS DISEASES (CSGID) REVDAT 5 20-SEP-23 4MUQ 1 REMARK SEQADV LINK REVDAT 4 14-MAY-14 4MUQ 1 JRNL REVDAT 3 23-APR-14 4MUQ 1 JRNL REVDAT 2 22-JAN-14 4MUQ 1 REMARK REVDAT 1 09-OCT-13 4MUQ 0 JRNL AUTH D.MEZIANE-CHERIF,P.J.STOGIOS,E.EVDOKIMOVA,A.SAVCHENKO, JRNL AUTH 2 P.COURVALIN JRNL TITL STRUCTURAL BASIS FOR THE EVOLUTION OF VANCOMYCIN RESISTANCE JRNL TITL 2 D,D-PEPTIDASES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 5872 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24711382 JRNL DOI 10.1073/PNAS.1402259111 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 54882 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2678 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.4102 - 4.2374 0.98 3417 212 0.1547 0.1494 REMARK 3 2 4.2374 - 3.3640 1.00 3480 176 0.1349 0.1348 REMARK 3 3 3.3640 - 2.9389 1.00 3494 200 0.1574 0.1967 REMARK 3 4 2.9389 - 2.6703 0.99 3518 205 0.1589 0.2198 REMARK 3 5 2.6703 - 2.4789 0.99 3456 194 0.1591 0.2080 REMARK 3 6 2.4789 - 2.3328 0.99 3476 205 0.1574 0.1878 REMARK 3 7 2.3328 - 2.2160 0.99 3462 224 0.1470 0.1714 REMARK 3 8 2.2160 - 2.1195 0.98 3493 138 0.1431 0.1631 REMARK 3 9 2.1195 - 2.0379 0.98 3405 188 0.1506 0.1897 REMARK 3 10 2.0379 - 1.9676 0.98 3495 163 0.1512 0.1801 REMARK 3 11 1.9676 - 1.9061 0.98 3456 178 0.1656 0.1691 REMARK 3 12 1.9061 - 1.8516 0.97 3373 192 0.1514 0.2025 REMARK 3 13 1.8516 - 1.8029 0.97 3465 164 0.1650 0.1905 REMARK 3 14 1.8029 - 1.7589 0.97 3393 175 0.1569 0.2055 REMARK 3 15 1.7589 - 1.7189 0.97 3364 198 0.1613 0.1830 REMARK 3 16 1.7189 - 1.6823 0.96 3339 177 0.1638 0.1952 REMARK 3 17 1.6823 - 1.6487 0.96 3437 199 0.1651 0.1767 REMARK 3 18 1.6487 - 1.6175 0.96 3292 183 0.1726 0.1901 REMARK 3 19 1.6175 - 1.5887 0.96 3424 179 0.1741 0.2136 REMARK 3 20 1.5887 - 1.5617 0.95 3339 183 0.1795 0.1722 REMARK 3 21 1.5617 - 1.5365 0.95 3350 180 0.1998 0.2050 REMARK 3 22 1.5365 - 1.5129 0.96 3311 189 0.1920 0.2073 REMARK 3 23 1.5129 - 1.4906 0.95 3334 183 0.2113 0.2475 REMARK 3 24 1.4906 - 1.4697 0.95 3365 150 0.2126 0.2286 REMARK 3 25 1.4697 - 1.4498 0.95 3287 205 0.2237 0.2495 REMARK 3 26 1.4498 - 1.4310 0.94 3343 153 0.2356 0.2540 REMARK 3 27 1.4310 - 1.4131 0.94 3359 129 0.2529 0.2814 REMARK 3 28 1.4131 - 1.3960 0.94 3280 211 0.2645 0.2679 REMARK 3 29 1.3960 - 1.3798 0.94 3332 186 0.2884 0.3063 REMARK 3 30 1.3798 - 1.3643 0.92 3231 134 0.3060 0.3368 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.014 2251 REMARK 3 ANGLE : 1.397 3047 REMARK 3 CHIRALITY : 0.085 311 REMARK 3 PLANARITY : 0.005 393 REMARK 3 DIHEDRAL : 14.795 909 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESI 0:50 REMARK 3 ORIGIN FOR THE GROUP (A): 19.2349 -10.5123 20.9115 REMARK 3 T TENSOR REMARK 3 T11: 0.1574 T22: 0.1327 REMARK 3 T33: 0.1034 T12: -0.0012 REMARK 3 T13: 0.0101 T23: 0.0314 REMARK 3 L TENSOR REMARK 3 L11: 1.1151 L22: 1.3239 REMARK 3 L33: 1.5051 L12: 0.2552 REMARK 3 L13: 0.6298 L23: 0.1855 REMARK 3 S TENSOR REMARK 3 S11: -0.0318 S12: -0.3241 S13: -0.2004 REMARK 3 S21: 0.2455 S22: 0.0431 S23: 0.0397 REMARK 3 S31: 0.2242 S32: -0.1121 S33: -0.0403 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESI 51:116 REMARK 3 ORIGIN FOR THE GROUP (A): 15.4008 -1.8318 8.2152 REMARK 3 T TENSOR REMARK 3 T11: 0.0713 T22: 0.0485 REMARK 3 T33: 0.0981 T12: 0.0013 REMARK 3 T13: -0.0119 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 1.2257 L22: 1.5412 REMARK 3 L33: 2.6519 L12: -0.0867 REMARK 3 L13: -0.6046 L23: 0.6849 REMARK 3 S TENSOR REMARK 3 S11: 0.0136 S12: -0.0215 S13: 0.0627 REMARK 3 S21: -0.1022 S22: -0.0188 S23: 0.0952 REMARK 3 S31: -0.0499 S32: -0.1137 S33: -0.0050 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESI 117:194 REMARK 3 ORIGIN FOR THE GROUP (A): 20.4608 6.6519 15.4580 REMARK 3 T TENSOR REMARK 3 T11: 0.1088 T22: 0.0602 REMARK 3 T33: 0.1116 T12: -0.0050 REMARK 3 T13: 0.0099 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 2.7070 L22: 2.6735 REMARK 3 L33: 2.7613 L12: -0.7156 REMARK 3 L13: -0.0419 L23: -0.2716 REMARK 3 S TENSOR REMARK 3 S11: 0.0317 S12: -0.0540 S13: 0.2680 REMARK 3 S21: -0.1244 S22: 0.0588 S23: 0.1040 REMARK 3 S31: -0.2705 S32: -0.1281 S33: -0.0550 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESI 195:250 REMARK 3 ORIGIN FOR THE GROUP (A): 29.0658 -5.4863 34.1969 REMARK 3 T TENSOR REMARK 3 T11: 0.2228 T22: 0.3489 REMARK 3 T33: 0.0706 T12: 0.0177 REMARK 3 T13: -0.0339 T23: 0.0094 REMARK 3 L TENSOR REMARK 3 L11: 3.1491 L22: 4.5232 REMARK 3 L33: 3.6684 L12: 0.1444 REMARK 3 L13: 0.5801 L23: -0.5077 REMARK 3 S TENSOR REMARK 3 S11: -0.0018 S12: -0.8262 S13: -0.0636 REMARK 3 S21: 0.8914 S22: 0.0540 S23: 0.0073 REMARK 3 S31: 0.3536 S32: 0.2134 S33: 0.0068 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4MUQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082389. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.27689 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54882 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 79.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.57800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 4F78 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 CACODYLATE AND 30% POLYETHYLENE GLYCOL (PEG) 8K, 75 MM PHY D-ALA- REMARK 280 D-ALA PHOSPHINATE ANALOG, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 273K, PH 6.3 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 21.86400 REMARK 290 SMTRY3 2 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 251 REMARK 465 THR A 252 REMARK 465 ASP A 253 REMARK 465 ASP A 254 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 ARG A 126 NE - CZ - NH1 ANGL. DEV. = 3.8 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 TYR A 131 35.95 -96.34 REMARK 500 ALA A 207 -141.70 36.19 REMARK 500 ASP A 222 -96.95 -119.50 REMARK 500 ASN A 231 40.76 -89.79 REMARK 500 ILE A 241 -59.15 -131.82 REMARK 500 ASP A 242 1.73 -152.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PE3 A 307 REMARK 610 PE3 A 308 REMARK 610 PE3 A 309 REMARK 610 PE3 A 310 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 107 NE2 REMARK 620 2 ASP A 114 OD1 106.0 REMARK 620 3 ASP A 114 OD2 87.8 57.7 REMARK 620 4 HIS A 167 ND1 100.1 97.3 155.0 REMARK 620 5 LY0 A 302 O32 147.1 100.4 90.0 95.7 REMARK 620 6 LY0 A 302 O31 81.8 138.9 83.0 121.5 65.4 REMARK 620 7 2D8 A 303 O32 147.2 100.3 90.0 95.7 0.1 65.4 REMARK 620 8 2D8 A 303 O31 81.9 138.6 82.7 121.7 65.3 0.3 65.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LY0 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2D8 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE3 A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE3 A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE3 A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE3 A 310 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F78 RELATED DB: PDB REMARK 900 APO CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE REMARK 900 VANXYG REMARK 900 RELATED ID: IDP91774 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: 4MUR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D,D- REMARK 900 PENTAPEPTIDASE VANXYC D59S MUTANT REMARK 900 RELATED ID: 4MUS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D,D- REMARK 900 PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALA-D-ALA REMARK 900 PHOSPHINATE ANALOG REMARK 900 RELATED ID: 4MUT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D,D- REMARK 900 PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALANINE REMARK 900 RELATED ID: 4OAK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D,D- REMARK 900 PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALANINE-D- REMARK 900 ALANINE AND COPPER (II) DBREF 4MUQ A 1 254 UNP Q9KHL8 Q9KHL8_ENTFL 1 254 SEQADV 4MUQ GLY A 0 UNP Q9KHL8 EXPRESSION TAG SEQRES 1 A 255 GLY MET MET LYS THR ILE GLU LEU GLU LYS GLU GLU ILE SEQRES 2 A 255 TYR CYS GLY ASN LEU LEU LEU VAL ASN LYS ASN TYR PRO SEQRES 3 A 255 LEU ARG ASP ASN ASN VAL LYS GLY LEU VAL PRO ALA ASP SEQRES 4 A 255 ILE ARG PHE PRO ASN ILE LEU MET LYS ARG ASP VAL ALA SEQRES 5 A 255 ASN VAL LEU GLN LEU ILE PHE GLU LYS ILE SER ALA GLY SEQRES 6 A 255 ASN SER ILE VAL PRO VAL SER GLY TYR ARG SER LEU GLU SEQRES 7 A 255 GLU GLN THR ALA ILE TYR ASP GLY SER LEU LYS ASP ASN SEQRES 8 A 255 GLY GLU ASP PHE THR ARG LYS TYR VAL ALA LEU PRO ASN SEQRES 9 A 255 HIS SER GLU HIS GLN THR GLY LEU ALA ILE ASP LEU GLY SEQRES 10 A 255 LEU ASN LYS LYS ASP ILE ASP PHE ILE ARG PRO ASP PHE SEQRES 11 A 255 PRO TYR ASP GLY ILE CYS ASP GLU PHE ARG ARG ALA ALA SEQRES 12 A 255 PRO ASP TYR GLY PHE THR GLN ARG TYR ALA ARG ASP LYS SEQRES 13 A 255 GLU GLU ILE THR GLY ILE SER HIS GLU PRO TRP HIS PHE SEQRES 14 A 255 ARG TYR VAL GLY TYR PRO HIS SER LYS ILE MET GLN GLU SEQRES 15 A 255 ASN GLY PHE SER LEU GLU GLU TYR THR GLN PHE ILE LYS SEQRES 16 A 255 ALA TYR LEU GLU ASP ASN LYS TYR LEU PHE GLU GLN ALA SEQRES 17 A 255 HIS ARG ALA GLU ILE GLU ILE TYR TYR VAL PRO ALA LYS SEQRES 18 A 255 ASP ASP LYS THR LEU ILE LYS ILE PRO GLU ASN CYS VAL SEQRES 19 A 255 TYR GLN ILE SER GLY ASN ASN ILE ASP GLY PHE VAL VAL SEQRES 20 A 255 THR ILE TRP ARG LYS THR ASP ASP HET ZN A 301 1 HET LY0 A 302 12 HET 2D8 A 303 12 HET EDO A 304 4 HET GOL A 305 6 HET GOL A 306 6 HET PE3 A 307 7 HET PE3 A 308 7 HET PE3 A 309 10 HET PE3 A 310 7 HETNAM ZN ZINC ION HETNAM LY0 (2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2- HETNAM 2 LY0 METHYLPROPANOIC ACID HETNAM 2D8 (2R)-3-[(R)-[(1S)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2- HETNAM 2 2D8 METHYLPROPANOIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM PE3 3,6,9,12,15,18,21,24,27,30,33,36,39- HETNAM 2 PE3 TRIDECAOXAHENTETRACONTANE-1,41-DIOL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN PE3 POLYETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 LY0 C6 H14 N O4 P FORMUL 4 2D8 C6 H14 N O4 P FORMUL 5 EDO C2 H6 O2 FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 PE3 4(C28 H58 O15) FORMUL 12 HOH *285(H2 O) HELIX 1 1 GLU A 10 CYS A 14 5 5 HELIX 2 2 ARG A 48 SER A 62 1 15 HELIX 3 3 SER A 75 GLY A 91 1 17 HELIX 4 4 GLY A 91 VAL A 99 1 9 HELIX 5 5 SER A 105 GLY A 110 5 6 HELIX 6 6 ASP A 132 ALA A 142 1 11 HELIX 7 7 PRO A 143 TYR A 145 5 3 HELIX 8 8 ALA A 152 ASP A 154 5 3 HELIX 9 9 LYS A 155 GLY A 160 1 6 HELIX 10 10 PRO A 174 GLY A 183 1 10 HELIX 11 11 SER A 185 LYS A 194 1 10 HELIX 12 12 ALA A 195 TYR A 196 5 2 HELIX 13 13 LEU A 197 LYS A 201 5 5 SHEET 1 A 2 MET A 2 GLU A 8 0 SHEET 2 A 2 LYS A 223 PRO A 229 -1 O ILE A 228 N LYS A 3 SHEET 1 B 2 LEU A 34 ASP A 38 0 SHEET 2 B 2 PHE A 41 LYS A 47 -1 O ILE A 44 N ALA A 37 SHEET 1 C 4 ILE A 67 SER A 71 0 SHEET 2 C 4 ALA A 112 LEU A 117 -1 O ASP A 114 N VAL A 70 SHEET 3 C 4 HIS A 167 TYR A 170 -1 O PHE A 168 N ILE A 113 SHEET 4 C 4 PHE A 147 GLN A 149 -1 N THR A 148 O ARG A 169 SHEET 1 D 4 TYR A 202 PHE A 204 0 SHEET 2 D 4 ILE A 212 PRO A 218 -1 O ILE A 212 N PHE A 204 SHEET 3 D 4 GLY A 243 TRP A 249 -1 O ILE A 248 N GLU A 213 SHEET 4 D 4 VAL A 233 GLY A 238 -1 N VAL A 233 O TRP A 249 LINK NE2 HIS A 107 ZN ZN A 301 1555 1555 2.02 LINK OD1 ASP A 114 ZN ZN A 301 1555 1555 1.96 LINK OD2 ASP A 114 ZN ZN A 301 1555 1555 2.38 LINK ND1 HIS A 167 ZN ZN A 301 1555 1555 2.08 LINK ZN ZN A 301 O32ALY0 A 302 1555 1555 2.19 LINK ZN ZN A 301 O31ALY0 A 302 1555 1555 2.41 LINK ZN ZN A 301 O32B2D8 A 303 1555 1555 2.19 LINK ZN ZN A 301 O31B2D8 A 303 1555 1555 2.42 CISPEP 1 TYR A 173 PRO A 174 0 4.28 SITE 1 AC1 5 HIS A 107 ASP A 114 HIS A 167 LY0 A 302 SITE 2 AC1 5 2D8 A 303 SITE 1 AC2 13 ARG A 74 GLN A 79 TYR A 98 ALA A 100 SITE 2 AC2 13 SER A 105 HIS A 107 ASP A 114 ILE A 125 SITE 3 AC2 13 GLU A 164 TRP A 166 HIS A 167 ZN A 301 SITE 4 AC2 13 HOH A 419 SITE 1 AC3 13 ARG A 74 GLN A 79 TYR A 98 ALA A 100 SITE 2 AC3 13 SER A 105 HIS A 107 ASP A 114 ILE A 125 SITE 3 AC3 13 GLU A 164 TRP A 166 HIS A 167 ZN A 301 SITE 4 AC3 13 HOH A 419 SITE 1 AC4 6 LYS A 97 GLU A 156 ILE A 161 SER A 162 SITE 2 AC4 6 HOH A 587 HOH A 671 SITE 1 AC5 4 ARG A 153 ASP A 154 HOH A 627 HOH A 656 SITE 1 AC6 3 ASN A 65 SER A 66 HOH A 606 SITE 1 AC7 8 ASN A 21 LYS A 22 ASN A 23 ARG A 40 SITE 2 AC7 8 GLU A 157 ILE A 158 THR A 159 HOH A 502 SITE 1 AC8 3 VAL A 233 TYR A 234 GLN A 235 SITE 1 AC9 7 LEU A 87 LYS A 88 ASN A 90 GLY A 91 SITE 2 AC9 7 GLU A 92 ASP A 93 HOH A 452 SITE 1 BC1 3 LYS A 32 GLY A 33 ARG A 48 CRYST1 38.895 43.728 80.236 90.00 99.20 90.00 P 1 21 1 2 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 0.025710 0.000000 0.004164 0.00000 SCALE2 0.000000 0.022869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012626 0.00000