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 7 20-NOV-24 4F78 1 REMARK SEQADV LINK
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-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) : 1.95
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.58
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4
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 DEPOSITION ID IS D_1000072542.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
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 ASN A 200 59.19 -151.60
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 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 95.7
REMARK 620 3 ASP A 114 OD2 83.3 55.2
REMARK 620 4 HIS A 167 ND1 101.5 91.9 147.1
REMARK 620 5 SO4 A 303 O2 80.2 151.7 96.5 116.4
REMARK 620 6 HOH A 418 O 158.1 99.2 92.2 94.0 79.0
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 VANXYG
REMARK 900 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/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 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 NE2 HIS A 107 ZN ZN A 301 1555 1555 2.23
LINK OD1 ASP A 114 ZN ZN A 301 1555 1555 2.18
LINK OD2 ASP A 114 ZN ZN A 301 1555 1555 2.56
LINK ND1 HIS A 167 ZN ZN A 301 1555 1555 2.19
LINK ZN ZN A 301 O2 SO4 A 303 1555 1555 2.70
LINK ZN ZN A 301 O HOH A 418 1555 1555 2.21
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