HEADER HYDROLASE 15-MAY-12 4F78 TITLE CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE VANXYG COMPND MOL_ID: 1; COMPND 2 MOLECULE: D,D-DIPEPTIDASE/D,D-CARBOXYPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D,D-PEPTIDASE, VANXYG; COMPND 5 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: P15TV 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, D-ALANINE-D-ALANINE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.J.STOGIOS,Z.WAWRZAK,E.EVDOKIMOVA,G.MINASOV,O.EGOROVA,R.DI LEO, AUTHOR 2 M.KUDRITSKA,V.YIM,D.MEZIANE-CHERIF,P.COURVALIN,A.SAVCHENKO, AUTHOR 3 W.F.ANDERSON,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES AUTHOR 4 (CSGID) REVDAT 6 14-MAY-14 4F78 1 JRNL REVDAT 5 23-APR-14 4F78 1 JRNL REVDAT 4 22-JAN-14 4F78 1 REMARK REVDAT 3 16-OCT-13 4F78 1 TITLE REVDAT 2 02-OCT-13 4F78 1 KEYWDS REMARK REVDAT 1 23-MAY-12 4F78 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. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 19734 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 949 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 39.5926 - 4.5829 0.98 2738 144 0.1596 0.1556 REMARK 3 2 4.5829 - 3.6384 0.99 2756 147 0.1227 0.1564 REMARK 3 3 3.6384 - 3.1787 0.99 2772 145 0.1439 0.1718 REMARK 3 4 3.1787 - 2.8882 0.99 2758 153 0.1497 0.1934 REMARK 3 5 2.8882 - 2.6812 0.99 2757 152 0.1515 0.1882 REMARK 3 6 2.6812 - 2.5232 0.99 2757 136 0.1529 0.1956 REMARK 3 7 2.5232 - 2.3968 0.98 2766 151 0.1580 0.2262 REMARK 3 8 2.3968 - 2.2925 0.98 2673 151 0.1557 0.1972 REMARK 3 9 2.2925 - 2.2043 0.98 2811 146 0.1600 0.2152 REMARK 3 10 2.2043 - 2.1282 0.98 2715 137 0.1596 0.2052 REMARK 3 11 2.1282 - 2.0617 0.98 2768 144 0.1755 0.2173 REMARK 3 12 2.0617 - 2.0027 0.98 2708 146 0.1947 0.2068 REMARK 3 13 2.0027 - 1.9500 0.98 2747 123 0.2171 0.2775 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 48.65 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.500 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) : -1.71430 REMARK 3 B22 (A**2) : 1.34940 REMARK 3 B33 (A**2) : 0.36480 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.27790 REMARK 3 B23 (A**2) : -0.00000 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 : 0.016 2201 REMARK 3 ANGLE : 1.494 2966 REMARK 3 CHIRALITY : 0.116 310 REMARK 3 PLANARITY : 0.007 386 REMARK 3 DIHEDRAL : 14.268 840 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): -13.4764 -13.8820 -18.1936 REMARK 3 T TENSOR REMARK 3 T11: 0.1352 T22: 0.1233 REMARK 3 T33: 0.1346 T12: -0.0144 REMARK 3 T13: 0.0118 T23: 0.0325 REMARK 3 L TENSOR REMARK 3 L11: 0.3823 L22: 0.7702 REMARK 3 L33: 1.4629 L12: 0.0117 REMARK 3 L13: 0.5165 L23: -0.0827 REMARK 3 S TENSOR REMARK 3 S11: -0.0166 S12: -0.3294 S13: -0.2666 REMARK 3 S21: 0.1715 S22: 0.0401 S23: 0.1086 REMARK 3 S31: 0.1831 S32: -0.0589 S33: -0.0657 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain A and resi 51:116 REMARK 3 ORIGIN FOR THE GROUP (A): -17.2558 -5.3482 -31.1827 REMARK 3 T TENSOR REMARK 3 T11: 0.0502 T22: 0.0542 REMARK 3 T33: 0.1032 T12: -0.0142 REMARK 3 T13: -0.0138 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 1.0575 L22: 1.6291 REMARK 3 L33: 3.0137 L12: -0.4240 REMARK 3 L13: -0.5374 L23: 0.7564 REMARK 3 S TENSOR REMARK 3 S11: 0.0413 S12: -0.0201 S13: 0.0131 REMARK 3 S21: -0.0517 S22: -0.0586 S23: 0.0985 REMARK 3 S31: 0.0093 S32: -0.1347 S33: 0.0057 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: chain A and resi 117:194 REMARK 3 ORIGIN FOR THE GROUP (A): -11.8754 3.1163 -23.7725 REMARK 3 T TENSOR REMARK 3 T11: 0.0715 T22: 0.0411 REMARK 3 T33: 0.0841 T12: -0.0035 REMARK 3 T13: 0.0197 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 2.6162 L22: 2.2842 REMARK 3 L33: 2.1523 L12: -0.6600 REMARK 3 L13: -0.0608 L23: -0.2919 REMARK 3 S TENSOR REMARK 3 S11: 0.0153 S12: -0.0502 S13: 0.1704 REMARK 3 S21: -0.0675 S22: 0.0561 S23: 0.0946 REMARK 3 S31: -0.2049 S32: -0.1041 S33: -0.0282 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: chain A and resi 195:250 REMARK 3 ORIGIN FOR THE GROUP (A): -3.1852 -8.8349 -5.4101 REMARK 3 T TENSOR REMARK 3 T11: 0.1725 T22: 0.2656 REMARK 3 T33: 0.0305 T12: 0.0405 REMARK 3 T13: -0.0385 T23: 0.0223 REMARK 3 L TENSOR REMARK 3 L11: 2.7849 L22: 3.8666 REMARK 3 L33: 3.0980 L12: 0.4257 REMARK 3 L13: 0.4265 L23: -0.5094 REMARK 3 S TENSOR REMARK 3 S11: -0.0539 S12: -0.6402 S13: -0.0715 REMARK 3 S21: 0.7326 S22: -0.0311 S23: 0.0969 REMARK 3 S31: 0.2433 S32: -0.0655 S33: 0.0156 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 4F78 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-12. REMARK 100 THE RCSB ID CODE IS RCSB072542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-11 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) : 0.97918 REMARK 200 MONOCHROMATOR : SI {1,1,1} REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19747 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 79.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.32900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX (PHENIX.AUTOSOL) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 CACODYLATE, 30% PEG 8K, PH 6.3, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 21.98000 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: 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 O4 SO4 A 303 O HOH A 483 2.17 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 ASP A 121 51.54 -93.20 REMARK 500 TYR A 131 39.91 -96.39 REMARK 500 HIS A 163 122.11 -37.40 REMARK 500 ASN A 200 67.33 -155.63 REMARK 500 GLN A 206 -79.85 -103.08 REMARK 500 ALA A 207 105.97 -177.20 REMARK 500 HIS A 208 117.57 -26.39 REMARK 500 ARG A 209 -140.97 56.21 REMARK 500 ASP A 222 -96.12 -116.75 REMARK 500 ASN A 231 39.66 -78.69 REMARK 500 ILE A 241 -58.31 -127.26 REMARK 500 ASP A 242 -0.20 -155.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG A 209 23.6 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 114 OD1 REMARK 620 2 HIS A 167 ND1 91.9 REMARK 620 3 HOH A 418 O 99.2 94.0 REMARK 620 4 HIS A 107 NE2 95.7 101.5 158.1 REMARK 620 5 ASP A 114 OD2 55.2 147.1 92.2 83.3 REMARK 620 6 SO4 A 303 O2 151.7 116.4 79.0 80.2 96.5 REMARK 620 N 1 2 3 4 5 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 CL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 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 EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 316 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP91774 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: 4MUQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE REMARK 900 VANXYG IN COMPLEX WITH D-ALA-D-ALA PHOSPHINATE ANALOG REMARK 900 RELATED ID: 4MUR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/ REMARK 900 D,D-PENTAPEPTIDASE VANXYC D59S MUTANT REMARK 900 RELATED ID: 4MUS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/ REMARK 900 D,D-PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALA REMARK 900 -D-ALA PHOSPHINATE ANALOG REMARK 900 RELATED ID: 4MUT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/ REMARK 900 D,D-PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D- REMARK 900 ALANINE REMARK 900 RELATED ID: 4OAK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/ REMARK 900 D,D-PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D- REMARK 900 ALANINE-D-ALANINE AND COPPER (II) DBREF 4F78 A 1 254 UNP Q9KHL8 Q9KHL8_ENTFL 1 254 SEQADV 4F78 GLY A 0 UNP Q9KHL8 EXPRESSION TAG SEQRES 1 A 255 GLY MSE MSE 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 MSE 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 MSE 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 MODRES 4F78 MSE A 1 MET SELENOMETHIONINE MODRES 4F78 MSE A 2 MET SELENOMETHIONINE MODRES 4F78 MSE A 46 MET SELENOMETHIONINE MODRES 4F78 MSE A 179 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 2 8 HET MSE A 46 16 HET MSE A 179 8 HET ZN A 301 1 HET CL A 302 1 HET SO4 A 303 5 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET EDO A 308 4 HET EDO A 309 4 HET EDO A 310 4 HET EDO A 311 4 HET EDO A 312 4 HET EDO A 313 4 HET GOL A 314 6 HET GOL A 315 6 HET GOL A 316 6 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 CL CL 1- FORMUL 4 SO4 O4 S 2- FORMUL 5 EDO 10(C2 H6 O2) FORMUL 15 GOL 3(C3 H8 O3) FORMUL 18 HOH *187(H2 O) HELIX 1 1 GLU A 10 CYS A 14 5 5 HELIX 2 2 ARG A 48 ILE A 61 1 14 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 SHEET 1 A 2 MSE 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 PRO A 36 0 SHEET 2 B 2 LEU A 45 LYS A 47 -1 O MSE A 46 N VAL A 35 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 GLU A 205 0 SHEET 2 D 4 GLU A 211 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 C GLY A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N MSE A 2 1555 1555 1.33 LINK C MSE A 2 N LYS A 3 1555 1555 1.33 LINK C LEU A 45 N AMSE A 46 1555 1555 1.33 LINK C LEU A 45 N BMSE A 46 1555 1555 1.34 LINK C AMSE A 46 N LYS A 47 1555 1555 1.33 LINK C BMSE A 46 N LYS A 47 1555 1555 1.33 LINK C ILE A 178 N MSE A 179 1555 1555 1.33 LINK C MSE A 179 N GLN A 180 1555 1555 1.33 LINK OD1 ASP A 114 ZN ZN A 301 1555 1555 2.18 LINK ND1 HIS A 167 ZN ZN A 301 1555 1555 2.19 LINK ZN ZN A 301 O HOH A 418 1555 1555 2.21 LINK NE2 HIS A 107 ZN ZN A 301 1555 1555 2.23 LINK OD2 ASP A 114 ZN ZN A 301 1555 1555 2.56 LINK ZN ZN A 301 O2 SO4 A 303 1555 1555 2.70 CISPEP 1 TYR A 173 PRO A 174 0 4.71 CISPEP 2 HIS A 208 ARG A 209 0 -10.50 SITE 1 AC1 5 HIS A 107 ASP A 114 HIS A 167 SO4 A 303 SITE 2 AC1 5 HOH A 418 SITE 1 AC2 4 MSE A 2 LYS A 3 THR A 4 LYS A 227 SITE 1 AC3 11 ARG A 74 GLN A 79 VAL A 99 ALA A 100 SITE 2 AC3 11 SER A 105 HIS A 107 HIS A 167 ZN A 301 SITE 3 AC3 11 HOH A 424 HOH A 460 HOH A 483 SITE 1 AC4 3 LYS A 120 GLU A 157 EDO A 310 SITE 1 AC5 7 PRO A 36 ALA A 37 ASN A 52 GLN A 191 SITE 2 AC5 7 HOH A 442 HOH A 512 HOH A 516 SITE 1 AC6 3 GLU A 188 PHE A 192 HOH A 470 SITE 1 AC7 5 PRO A 218 EDO A 308 HOH A 431 HOH A 491 SITE 2 AC7 5 HOH A 524 SITE 1 AC8 2 ASP A 199 EDO A 307 SITE 1 AC9 4 ASN A 21 LYS A 22 ILE A 158 THR A 159 SITE 1 BC1 5 LYS A 97 GLY A 160 ILE A 161 SER A 162 SITE 2 BC1 5 EDO A 304 SITE 1 BC2 4 GLY A 91 GLU A 92 ASP A 93 HOH A 420 SITE 1 BC3 4 GLU A 181 PHE A 204 GLU A 205 HOH A 584 SITE 1 BC4 3 ASP A 144 ARG A 209 HOH A 531 SITE 1 BC5 3 ALA A 152 ARG A 153 ASP A 154 SITE 1 BC6 3 ASN A 65 SER A 66 LYS A 155 SITE 1 BC7 7 CYS A 14 GLY A 15 LEU A 18 VAL A 31 SITE 2 BC7 7 THR A 109 HOH A 578 HOH A 585 CRYST1 38.912 43.960 80.199 90.00 99.19 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 0.025699 0.000000 0.004159 0.00000 SCALE2 0.000000 0.022748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012631 0.00000