HEADER HYDROLASE 23-SEP-13 4MUR TITLE CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D,D- TITLE 2 PENTAPEPTIDASE VANXYC D59S MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: D,D-DIPEPTIDASE/D,D-CARBOXYPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: D,D-DIPEPTIDASE/D,D-CARBOXYPEPTIDASE VANXYC; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS GALLINARUM; SOURCE 3 ORGANISM_TAXID: 1353; SOURCE 4 STRAIN: BM4174; SOURCE 5 GENE: VANXYC; 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, D- KEYWDS 5 PENTAPEPTIDASE, VANCOMYCIN RESISTANCE, ANTIBIOTIC RESISTANCE, KEYWDS 6 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 6 20-SEP-23 4MUR 1 REMARK SEQADV LINK REVDAT 5 14-MAY-14 4MUR 1 JRNL REVDAT 4 23-APR-14 4MUR 1 JRNL REVDAT 3 22-JAN-14 4MUR 1 REMARK REVDAT 2 09-OCT-13 4MUR 1 KEYWDS REVDAT 1 02-OCT-13 4MUR 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. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.3_1479) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 46109 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 2480 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 34.4568 - 5.1216 0.98 3162 137 0.1491 0.1867 REMARK 3 2 5.1216 - 4.0672 0.98 3116 193 0.1190 0.1624 REMARK 3 3 4.0672 - 3.5537 0.99 3205 169 0.1230 0.1567 REMARK 3 4 3.5537 - 3.2290 0.98 3098 162 0.1327 0.1791 REMARK 3 5 3.2290 - 2.9977 0.98 3115 171 0.1494 0.2005 REMARK 3 6 2.9977 - 2.8211 0.98 3163 156 0.1561 0.1919 REMARK 3 7 2.8211 - 2.6799 0.98 3181 158 0.1584 0.2057 REMARK 3 8 2.6799 - 2.5632 0.98 3124 171 0.1569 0.1910 REMARK 3 9 2.5632 - 2.4646 0.98 3112 164 0.1563 0.2260 REMARK 3 10 2.4646 - 2.3796 0.98 3126 202 0.1470 0.1953 REMARK 3 11 2.3796 - 2.3052 0.98 3115 167 0.1486 0.2119 REMARK 3 12 2.3052 - 2.2393 0.97 3061 159 0.1592 0.1978 REMARK 3 13 2.2393 - 2.1804 0.98 3167 194 0.1599 0.2305 REMARK 3 14 2.1804 - 2.1272 0.97 3033 160 0.1543 0.2095 REMARK 3 15 2.1272 - 2.0788 0.97 3133 145 0.1643 0.2394 REMARK 3 16 2.0788 - 2.0346 0.96 3083 154 0.1716 0.2222 REMARK 3 17 2.0346 - 1.9939 0.97 3138 171 0.1681 0.2204 REMARK 3 18 1.9939 - 1.9563 0.97 2992 176 0.1796 0.2105 REMARK 3 19 1.9563 - 1.9213 0.96 3130 161 0.1736 0.2066 REMARK 3 20 1.9213 - 1.8888 0.96 3083 158 0.1683 0.1622 REMARK 3 21 1.8888 - 1.8583 0.96 3053 177 0.1695 0.2183 REMARK 3 22 1.8583 - 1.8297 0.95 3051 206 0.1841 0.2149 REMARK 3 23 1.8297 - 1.8028 0.94 2925 172 0.1913 0.2427 REMARK 3 24 1.8028 - 1.7774 0.92 3012 138 0.2120 0.2359 REMARK 3 25 1.7774 - 1.7534 0.94 2968 184 0.2028 0.2424 REMARK 3 26 1.7534 - 1.7306 0.92 2867 152 0.2106 0.2758 REMARK 3 27 1.7306 - 1.7090 0.93 3057 171 0.2273 0.2559 REMARK 3 28 1.7090 - 1.6884 0.91 2900 170 0.2357 0.2536 REMARK 3 29 1.6884 - 1.6688 0.93 3000 145 0.2480 0.2772 REMARK 3 30 1.6688 - 1.6500 0.83 2578 149 0.2791 0.3416 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.450 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 : 0.012 3385 REMARK 3 ANGLE : 1.072 4614 REMARK 3 CHIRALITY : 0.071 479 REMARK 3 PLANARITY : 0.005 598 REMARK 3 DIHEDRAL : 15.522 1310 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESI 1:19 REMARK 3 ORIGIN FOR THE GROUP (A): 32.7963 15.4531 23.8010 REMARK 3 T TENSOR REMARK 3 T11: 0.1575 T22: 0.1247 REMARK 3 T33: 0.2366 T12: 0.0127 REMARK 3 T13: 0.0329 T23: 0.0316 REMARK 3 L TENSOR REMARK 3 L11: 0.0350 L22: 0.0315 REMARK 3 L33: 0.0008 L12: -0.0493 REMARK 3 L13: -0.0156 L23: 0.0015 REMARK 3 S TENSOR REMARK 3 S11: -0.0333 S12: 0.2920 S13: 0.2431 REMARK 3 S21: 0.1668 S22: 0.1025 S23: 0.2213 REMARK 3 S31: 0.0729 S32: -0.1424 S33: 0.0014 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESI 20:76 REMARK 3 ORIGIN FOR THE GROUP (A): 35.0033 1.7446 34.5365 REMARK 3 T TENSOR REMARK 3 T11: 0.0890 T22: 0.0761 REMARK 3 T33: 0.1082 T12: 0.0031 REMARK 3 T13: -0.0095 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.5114 L22: 0.1795 REMARK 3 L33: 0.3982 L12: 0.3502 REMARK 3 L13: -0.4886 L23: -0.1946 REMARK 3 S TENSOR REMARK 3 S11: 0.0307 S12: 0.0847 S13: -0.0166 REMARK 3 S21: 0.0755 S22: -0.0115 S23: 0.0852 REMARK 3 S31: 0.0037 S32: -0.0717 S33: 0.0413 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESI 77:124 REMARK 3 ORIGIN FOR THE GROUP (A): 44.2942 6.3561 37.7111 REMARK 3 T TENSOR REMARK 3 T11: 0.1284 T22: 0.0964 REMARK 3 T33: 0.1260 T12: 0.0118 REMARK 3 T13: -0.0079 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.1355 L22: 0.1946 REMARK 3 L33: 0.0348 L12: 0.1886 REMARK 3 L13: -0.1896 L23: 0.0370 REMARK 3 S TENSOR REMARK 3 S11: 0.0707 S12: -0.0400 S13: -0.0029 REMARK 3 S21: 0.1023 S22: -0.0398 S23: 0.0033 REMARK 3 S31: -0.0152 S32: 0.0173 S33: 0.0176 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESI 125:189 REMARK 3 ORIGIN FOR THE GROUP (A): 46.4593 6.6865 20.4984 REMARK 3 T TENSOR REMARK 3 T11: 0.0780 T22: 0.0811 REMARK 3 T33: 0.0767 T12: -0.0013 REMARK 3 T13: 0.0056 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.1074 L22: 0.2241 REMARK 3 L33: 0.4018 L12: 0.0449 REMARK 3 L13: -0.1515 L23: -0.0768 REMARK 3 S TENSOR REMARK 3 S11: -0.0106 S12: 0.0453 S13: -0.0183 REMARK 3 S21: -0.0324 S22: -0.0037 S23: -0.0430 REMARK 3 S31: -0.0062 S32: -0.0112 S33: -0.0477 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND RESI 1:18 REMARK 3 ORIGIN FOR THE GROUP (A): 12.9760 7.2918 50.0944 REMARK 3 T TENSOR REMARK 3 T11: 0.1623 T22: 0.1590 REMARK 3 T33: 0.1570 T12: 0.0005 REMARK 3 T13: -0.0267 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.0219 L22: 0.0019 REMARK 3 L33: 0.0031 L12: -0.0050 REMARK 3 L13: 0.0235 L23: -0.0071 REMARK 3 S TENSOR REMARK 3 S11: -0.0196 S12: 0.0491 S13: 0.0101 REMARK 3 S21: 0.0841 S22: 0.0822 S23: 0.0848 REMARK 3 S31: -0.1542 S32: -0.1660 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND RESI 19:106 REMARK 3 ORIGIN FOR THE GROUP (A): 27.8855 0.9918 47.6558 REMARK 3 T TENSOR REMARK 3 T11: 0.0716 T22: 0.0605 REMARK 3 T33: 0.0659 T12: 0.0010 REMARK 3 T13: -0.0074 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.7613 L22: 0.1205 REMARK 3 L33: 0.6190 L12: 0.0069 REMARK 3 L13: -0.6078 L23: 0.0091 REMARK 3 S TENSOR REMARK 3 S11: 0.0145 S12: -0.0714 S13: 0.0214 REMARK 3 S21: -0.0213 S22: -0.0108 S23: 0.0692 REMARK 3 S31: -0.0409 S32: 0.1685 S33: -0.0185 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN B AND RESI 107:117 REMARK 3 ORIGIN FOR THE GROUP (A): 34.4754 -11.1398 47.4335 REMARK 3 T TENSOR REMARK 3 T11: 0.2970 T22: 0.2853 REMARK 3 T33: 0.3156 T12: 0.1061 REMARK 3 T13: -0.0100 T23: -0.0083 REMARK 3 L TENSOR REMARK 3 L11: 0.0030 L22: 0.0081 REMARK 3 L33: 0.0041 L12: -0.0155 REMARK 3 L13: -0.0036 L23: 0.0239 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: 0.0647 S13: -0.1384 REMARK 3 S21: -0.0440 S22: -0.0893 S23: -0.0654 REMARK 3 S31: 0.0318 S32: 0.0170 S33: 0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN B AND RESI 118:189 REMARK 3 ORIGIN FOR THE GROUP (A): 19.9905 -2.3617 62.1564 REMARK 3 T TENSOR REMARK 3 T11: 0.1097 T22: 0.1553 REMARK 3 T33: 0.0815 T12: -0.0091 REMARK 3 T13: 0.0019 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.2276 L22: 0.1620 REMARK 3 L33: 0.6949 L12: -0.1731 REMARK 3 L13: -0.2371 L23: -0.2312 REMARK 3 S TENSOR REMARK 3 S11: 0.0154 S12: -0.2160 S13: -0.0673 REMARK 3 S21: -0.0440 S22: -0.0302 S23: -0.0050 REMARK 3 S31: 0.0868 S32: 0.0199 S33: -0.0512 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 4MUR 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_1000082390. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 1.27696 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 : 50465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 40.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.51200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 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 (%): 43.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MAGNESIUM CHLORIDE, 0.05 M MES, REMARK 280 20% PEG 8K, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 273K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 300 REMARK: DIMER IS IN THE ASYMMETRIC UNIT. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -178.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 ARG A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 GLY A 0 REMARK 465 ALA A 190 REMARK 465 MET B -20 REMARK 465 GLY B -19 REMARK 465 SER B -18 REMARK 465 SER B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 SER B -10 REMARK 465 SER B -9 REMARK 465 GLY B -8 REMARK 465 ARG B -7 REMARK 465 GLU B -6 REMARK 465 ASN B -5 REMARK 465 LEU B -4 REMARK 465 TYR B -3 REMARK 465 PHE B -2 REMARK 465 GLN B -1 REMARK 465 GLY B 0 REMARK 465 ALA B 190 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 PHE A 118 47.90 -149.89 REMARK 500 ASP B 110 80.46 49.97 REMARK 500 PHE B 118 58.87 -149.17 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 205 REMARK 610 PE3 A 206 REMARK 610 PE3 A 207 REMARK 610 PE3 A 208 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 NE2 REMARK 620 2 ASP A 102 OD1 111.0 REMARK 620 3 ASP A 102 OD2 92.0 61.5 REMARK 620 4 HIS A 156 ND1 105.6 86.8 147.8 REMARK 620 5 HOH A 383 O 146.2 100.5 92.5 87.6 REMARK 620 6 HOH A 465 O 73.6 116.0 54.5 156.2 81.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 95 NE2 REMARK 620 2 ASP B 102 OD1 98.9 REMARK 620 3 HIS B 156 ND1 116.3 102.6 REMARK 620 4 HOH B 385 O 142.3 100.2 90.7 REMARK 620 N 1 2 3 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE3 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE3 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE3 A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE3 A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP91778 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: 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) REMARK 900 RELATED ID: 4F78 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE BIFUNCTIONAL D,D- REMARK 900 DIPEPTIDASE/D,D-CARBOXYPEPTIDASE VANXYG FROM ENTEROCOCCUS FAECALIS DBREF 4MUR A 1 190 UNP Q9JN36 Q9JN36_ENTGA 1 190 DBREF 4MUR B 1 190 UNP Q9JN36 Q9JN36_ENTGA 1 190 SEQADV 4MUR MET A -20 UNP Q9JN36 INITIATING METHIONINE SEQADV 4MUR GLY A -19 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR SER A -18 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR SER A -17 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS A -16 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS A -15 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS A -14 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS A -13 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS A -12 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS A -11 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR SER A -10 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR SER A -9 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR GLY A -8 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR ARG A -7 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR GLU A -6 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR ASN A -5 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR LEU A -4 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR TYR A -3 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR PHE A -2 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR GLN A -1 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR GLY A 0 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR SER A 59 UNP Q9JN36 ASP 59 ENGINEERED MUTATION SEQADV 4MUR MET B -20 UNP Q9JN36 INITIATING METHIONINE SEQADV 4MUR GLY B -19 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR SER B -18 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR SER B -17 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS B -16 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS B -15 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS B -14 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS B -13 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS B -12 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR HIS B -11 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR SER B -10 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR SER B -9 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR GLY B -8 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR ARG B -7 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR GLU B -6 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR ASN B -5 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR LEU B -4 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR TYR B -3 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR PHE B -2 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR GLN B -1 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR GLY B 0 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUR SER B 59 UNP Q9JN36 ASP 59 ENGINEERED MUTATION SEQRES 1 A 211 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 211 ARG GLU ASN LEU TYR PHE GLN GLY MET ASN THR LEU GLN SEQRES 3 A 211 LEU ILE ASN LYS ASN HIS PRO LEU LYS LYS ASN GLN GLU SEQRES 4 A 211 PRO PRO HIS LEU VAL LEU ALA PRO PHE SER ASP HIS ASP SEQRES 5 A 211 VAL TYR LEU GLN PRO GLU VAL ALA LYS GLN TRP GLU ARG SEQRES 6 A 211 LEU VAL ARG ALA THR GLY LEU GLU LYS ASP ILE ARG LEU SEQRES 7 A 211 VAL SER GLY TYR ARG THR GLU LYS GLU GLN ARG ARG LEU SEQRES 8 A 211 TRP GLU TYR SER LEU LYS GLU ASN GLY LEU ALA TYR THR SEQRES 9 A 211 LYS GLN PHE VAL ALA LEU PRO GLY CYS SER GLU HIS GLN SEQRES 10 A 211 ILE GLY LEU ALA ILE ASP VAL GLY LEU LYS LYS GLN GLU SEQRES 11 A 211 ASP ASP ASP LEU ILE CYS PRO HIS PHE ARG ASP SER ALA SEQRES 12 A 211 ALA ALA ASP LEU PHE MET GLN GLN MET MET ASN TYR GLY SEQRES 13 A 211 PHE ILE LEU ARG TYR PRO GLU ASP LYS GLN GLU ILE THR SEQRES 14 A 211 GLY ILE SER TYR GLU PRO TRP HIS PHE ARG TYR VAL GLY SEQRES 15 A 211 LEU PRO HIS SER GLN VAL ILE THR ALA GLN LYS TRP THR SEQRES 16 A 211 LEU GLU GLU TYR HIS ASP TYR LEU ALA GLN THR VAL ARG SEQRES 17 A 211 GLN PHE ALA SEQRES 1 B 211 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 211 ARG GLU ASN LEU TYR PHE GLN GLY MET ASN THR LEU GLN SEQRES 3 B 211 LEU ILE ASN LYS ASN HIS PRO LEU LYS LYS ASN GLN GLU SEQRES 4 B 211 PRO PRO HIS LEU VAL LEU ALA PRO PHE SER ASP HIS ASP SEQRES 5 B 211 VAL TYR LEU GLN PRO GLU VAL ALA LYS GLN TRP GLU ARG SEQRES 6 B 211 LEU VAL ARG ALA THR GLY LEU GLU LYS ASP ILE ARG LEU SEQRES 7 B 211 VAL SER GLY TYR ARG THR GLU LYS GLU GLN ARG ARG LEU SEQRES 8 B 211 TRP GLU TYR SER LEU LYS GLU ASN GLY LEU ALA TYR THR SEQRES 9 B 211 LYS GLN PHE VAL ALA LEU PRO GLY CYS SER GLU HIS GLN SEQRES 10 B 211 ILE GLY LEU ALA ILE ASP VAL GLY LEU LYS LYS GLN GLU SEQRES 11 B 211 ASP ASP ASP LEU ILE CYS PRO HIS PHE ARG ASP SER ALA SEQRES 12 B 211 ALA ALA ASP LEU PHE MET GLN GLN MET MET ASN TYR GLY SEQRES 13 B 211 PHE ILE LEU ARG TYR PRO GLU ASP LYS GLN GLU ILE THR SEQRES 14 B 211 GLY ILE SER TYR GLU PRO TRP HIS PHE ARG TYR VAL GLY SEQRES 15 B 211 LEU PRO HIS SER GLN VAL ILE THR ALA GLN LYS TRP THR SEQRES 16 B 211 LEU GLU GLU TYR HIS ASP TYR LEU ALA GLN THR VAL ARG SEQRES 17 B 211 GLN PHE ALA HET ZN A 201 1 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HET PE3 A 205 6 HET PE3 A 206 6 HET PE3 A 207 6 HET PE3 A 208 7 HET ZN B 201 1 HET SO4 B 202 5 HET CL B 203 1 HET CL B 204 1 HET CL B 205 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM PE3 3,6,9,12,15,18,21,24,27,30,33,36,39- HETNAM 2 PE3 TRIDECAOXAHENTETRACONTANE-1,41-DIOL HETNAM SO4 SULFATE ION HETSYN PE3 POLYETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 CL 6(CL 1-) FORMUL 7 PE3 4(C28 H58 O15) FORMUL 12 SO4 O4 S 2- FORMUL 16 HOH *588(H2 O) HELIX 1 1 GLN A 35 GLY A 50 1 16 HELIX 2 2 THR A 63 GLY A 79 1 17 HELIX 3 3 GLY A 79 VAL A 87 1 9 HELIX 4 4 SER A 93 GLY A 98 5 6 HELIX 5 5 SER A 121 MET A 131 1 11 HELIX 6 6 MET A 132 TYR A 134 5 3 HELIX 7 7 LYS A 144 GLY A 149 1 6 HELIX 8 8 PRO A 163 GLN A 171 1 9 HELIX 9 9 THR A 174 GLN A 188 1 15 HELIX 10 10 GLN B 35 GLY B 50 1 16 HELIX 11 11 THR B 63 VAL B 87 1 25 HELIX 12 12 SER B 93 GLY B 98 5 6 HELIX 13 13 SER B 121 MET B 131 1 11 HELIX 14 14 MET B 132 TYR B 134 5 3 HELIX 15 15 LYS B 144 GLY B 149 1 6 HELIX 16 16 PRO B 163 LYS B 172 1 10 HELIX 17 17 THR B 174 PHE B 189 1 16 SHEET 1 A 2 VAL A 23 LEU A 24 0 SHEET 2 A 2 TYR A 33 LEU A 34 -1 O LEU A 34 N VAL A 23 SHEET 1 B 4 ILE A 55 SER A 59 0 SHEET 2 B 4 ALA A 100 LEU A 105 -1 O ASP A 102 N VAL A 58 SHEET 3 B 4 HIS A 156 TYR A 159 -1 O PHE A 157 N ILE A 101 SHEET 4 B 4 PHE A 136 LEU A 138 -1 N ILE A 137 O ARG A 158 SHEET 1 C 2 VAL B 23 LEU B 24 0 SHEET 2 C 2 TYR B 33 LEU B 34 -1 O LEU B 34 N VAL B 23 SHEET 1 D 4 ILE B 55 SER B 59 0 SHEET 2 D 4 ALA B 100 LEU B 105 -1 O ASP B 102 N VAL B 58 SHEET 3 D 4 HIS B 156 TYR B 159 -1 O PHE B 157 N ILE B 101 SHEET 4 D 4 PHE B 136 LEU B 138 -1 N ILE B 137 O ARG B 158 LINK NE2 HIS A 95 ZN ZN A 201 1555 1555 2.10 LINK OD1 ASP A 102 ZN ZN A 201 1555 1555 1.98 LINK OD2 ASP A 102 ZN ZN A 201 1555 1555 2.23 LINK ND1 HIS A 156 ZN ZN A 201 1555 1555 2.17 LINK ZN ZN A 201 O HOH A 383 1555 1555 2.08 LINK ZN ZN A 201 O HOH A 465 1555 1555 2.60 LINK NE2 HIS B 95 ZN ZN B 201 1555 1555 2.08 LINK OD1 ASP B 102 ZN ZN B 201 1555 1555 2.04 LINK ND1 HIS B 156 ZN ZN B 201 1555 1555 2.05 LINK ZN ZN B 201 O HOH B 385 1555 1555 2.06 CISPEP 1 LEU A 162 PRO A 163 0 -1.19 CISPEP 2 LEU B 162 PRO B 163 0 -0.10 SITE 1 AC1 5 HIS A 95 ASP A 102 HIS A 156 HOH A 383 SITE 2 AC1 5 HOH A 465 SITE 1 AC2 4 GLN A 67 ALA A 88 SER A 93 HOH A 598 SITE 1 AC3 3 ARG A 69 HOH A 528 LEU B 22 SITE 1 AC4 4 ASN A 8 ASN A 10 HIS A 11 HOH A 470 SITE 1 AC5 1 HIS A 179 SITE 1 AC6 5 MET A 1 ASN A 2 GLN A 5 LYS A 14 SITE 2 AC6 5 GLN A 17 SITE 1 AC7 4 GLU A 37 LYS A 40 GLN A 41 ARG A 44 SITE 1 AC8 4 PHE A 189 HIS B 179 ALA B 183 HOH B 574 SITE 1 AC9 5 HIS B 95 ASP B 102 HIS B 156 HOH B 353 SITE 2 AC9 5 HOH B 385 SITE 1 BC1 7 ARG A 119 LYS B 65 ARG B 68 ARG B 69 SITE 2 BC1 7 HOH B 411 HOH B 480 HOH B 563 SITE 1 BC2 3 GLN B 67 ALA B 88 HOH B 583 SITE 1 BC3 4 HIS A 21 LEU A 22 HOH A 580 ARG B 69 SITE 1 BC4 3 HOH A 538 THR B 63 HOH B 436 CRYST1 44.239 44.725 62.519 86.27 77.70 63.74 P 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 0.022604 -0.011152 -0.005303 0.00000 SCALE2 0.000000 0.024932 0.000831 0.00000 SCALE3 0.000000 0.000000 0.016380 0.00000