HEADER HYDROLASE 23-SEP-13 4MUT TITLE CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D,D- TITLE 2 PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D,D-DIPEPTIDASE/D,D-CARBOXYPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: VANXYC; COMPND 5 SYNONYM: D,D-DIPEPTIDASE/D,D-CARBOXYPEPTIDASE VANXYC; COMPND 6 ENGINEERED: YES; COMPND 7 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: 562; 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 5 20-SEP-23 4MUT 1 REMARK SEQADV LINK REVDAT 4 14-MAY-14 4MUT 1 JRNL REVDAT 3 23-APR-14 4MUT 1 JRNL REVDAT 2 22-JAN-14 4MUT 1 REMARK REVDAT 1 09-OCT-13 4MUT 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. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 20134 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 2053 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 34.5709 - 5.5419 0.99 2568 128 0.1301 0.1460 REMARK 3 2 5.5419 - 4.4016 0.99 2567 145 0.1116 0.1518 REMARK 3 3 4.4016 - 3.8460 0.99 2538 154 0.1200 0.1279 REMARK 3 4 3.8460 - 3.4948 0.99 2557 128 0.1329 0.1272 REMARK 3 5 3.4948 - 3.2445 0.99 2525 158 0.1497 0.1980 REMARK 3 6 3.2445 - 3.0533 0.99 2569 170 0.1668 0.2152 REMARK 3 7 3.0533 - 2.9005 0.98 2529 150 0.1847 0.1803 REMARK 3 8 2.9005 - 2.7743 0.98 2537 114 0.1927 0.2510 REMARK 3 9 2.7743 - 2.6675 0.98 2549 140 0.1972 0.2935 REMARK 3 10 2.6675 - 2.5755 0.98 2575 128 0.2137 0.2089 REMARK 3 11 2.5755 - 2.4950 0.98 2496 104 0.2200 0.2454 REMARK 3 12 2.4950 - 2.4237 0.98 2586 162 0.2281 0.2395 REMARK 3 13 2.4237 - 2.3599 0.97 2482 117 0.2424 0.2627 REMARK 3 14 2.3599 - 2.3023 0.97 2609 117 0.2588 0.3090 REMARK 3 15 2.3023 - 2.2500 0.97 2435 138 0.2780 0.3227 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.780 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 : 0.009 3248 REMARK 3 ANGLE : 1.129 4407 REMARK 3 CHIRALITY : 0.071 460 REMARK 3 PLANARITY : 0.007 573 REMARK 3 DIHEDRAL : 15.577 1225 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 2:19 REMARK 3 ORIGIN FOR THE GROUP (A): 34.2115 15.2912 22.1790 REMARK 3 T TENSOR REMARK 3 T11: 0.4272 T22: 0.3882 REMARK 3 T33: 0.4393 T12: 0.0197 REMARK 3 T13: 0.0254 T23: 0.0986 REMARK 3 L TENSOR REMARK 3 L11: 5.7046 L22: 9.5997 REMARK 3 L33: 9.1171 L12: -5.5848 REMARK 3 L13: -5.5224 L23: 7.3317 REMARK 3 S TENSOR REMARK 3 S11: -0.1053 S12: 0.8733 S13: 0.4400 REMARK 3 S21: 0.0700 S22: -0.2774 S23: 1.1985 REMARK 3 S31: 0.0403 S32: -1.0237 S33: 0.3697 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESI 20:76 REMARK 3 ORIGIN FOR THE GROUP (A): 36.6942 0.7164 32.6286 REMARK 3 T TENSOR REMARK 3 T11: 0.2484 T22: 0.2566 REMARK 3 T33: 0.1789 T12: -0.0301 REMARK 3 T13: 0.0780 T23: 0.0476 REMARK 3 L TENSOR REMARK 3 L11: 3.5512 L22: 6.0273 REMARK 3 L33: 4.3993 L12: 0.6287 REMARK 3 L13: -0.8795 L23: 2.1808 REMARK 3 S TENSOR REMARK 3 S11: 0.1199 S12: 0.0956 S13: 0.0427 REMARK 3 S21: 0.2476 S22: -0.2066 S23: 0.3495 REMARK 3 S31: -0.0446 S32: -0.2304 S33: 0.0721 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESI 77:124 REMARK 3 ORIGIN FOR THE GROUP (A): 45.9437 5.3677 35.6354 REMARK 3 T TENSOR REMARK 3 T11: 0.4173 T22: 0.3294 REMARK 3 T33: 0.2393 T12: -0.0220 REMARK 3 T13: 0.0322 T23: 0.0462 REMARK 3 L TENSOR REMARK 3 L11: 3.4044 L22: 4.0881 REMARK 3 L33: 1.9083 L12: -1.3479 REMARK 3 L13: -1.1547 L23: 2.7635 REMARK 3 S TENSOR REMARK 3 S11: -0.1155 S12: -0.2882 S13: -0.0424 REMARK 3 S21: 0.7932 S22: 0.1356 S23: -0.0001 REMARK 3 S31: 0.2181 S32: 0.2901 S33: -0.0433 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESI 125:188 REMARK 3 ORIGIN FOR THE GROUP (A): 47.6738 5.6631 18.7846 REMARK 3 T TENSOR REMARK 3 T11: 0.1785 T22: 0.3065 REMARK 3 T33: 0.1776 T12: -0.0276 REMARK 3 T13: 0.0723 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 4.3931 L22: 5.9218 REMARK 3 L33: 7.3739 L12: 0.0911 REMARK 3 L13: -0.2693 L23: -1.8429 REMARK 3 S TENSOR REMARK 3 S11: -0.0260 S12: 0.2548 S13: 0.2201 REMARK 3 S21: -0.3247 S22: -0.1002 S23: -0.2658 REMARK 3 S31: -0.2141 S32: 0.2086 S33: 0.1265 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND RESI 2:18 REMARK 3 ORIGIN FOR THE GROUP (A): 13.7578 5.8064 47.5140 REMARK 3 T TENSOR REMARK 3 T11: 0.3506 T22: 0.4256 REMARK 3 T33: 0.4790 T12: 0.0243 REMARK 3 T13: 0.0277 T23: 0.0491 REMARK 3 L TENSOR REMARK 3 L11: 8.5872 L22: 5.3101 REMARK 3 L33: 3.5269 L12: 1.0118 REMARK 3 L13: 5.4942 L23: 0.8156 REMARK 3 S TENSOR REMARK 3 S11: -0.3080 S12: 0.5824 S13: 1.0459 REMARK 3 S21: -0.1802 S22: 0.2323 S23: 1.0407 REMARK 3 S31: -0.9256 S32: -0.0480 S33: 0.1475 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND RESI 19:106 REMARK 3 ORIGIN FOR THE GROUP (A): 29.2208 -0.0275 45.7029 REMARK 3 T TENSOR REMARK 3 T11: 0.2545 T22: 0.2571 REMARK 3 T33: 0.1899 T12: -0.0129 REMARK 3 T13: 0.0804 T23: 0.0350 REMARK 3 L TENSOR REMARK 3 L11: 5.4756 L22: 2.3101 REMARK 3 L33: 7.1559 L12: 1.6659 REMARK 3 L13: 2.1358 L23: 2.0415 REMARK 3 S TENSOR REMARK 3 S11: 0.0373 S12: -0.1523 S13: 0.1240 REMARK 3 S21: 0.0928 S22: -0.0388 S23: -0.0106 REMARK 3 S31: -0.0118 S32: 0.5478 S33: 0.0046 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN B AND RESI 107:117 REMARK 3 ORIGIN FOR THE GROUP (A): 35.6338 -12.3528 44.7705 REMARK 3 T TENSOR REMARK 3 T11: 1.3165 T22: 1.5868 REMARK 3 T33: 1.1702 T12: 0.4532 REMARK 3 T13: -0.0005 T23: -0.2638 REMARK 3 L TENSOR REMARK 3 L11: 0.6607 L22: 7.0275 REMARK 3 L33: 0.6210 L12: 2.1280 REMARK 3 L13: 0.2766 L23: 0.5860 REMARK 3 S TENSOR REMARK 3 S11: 2.0927 S12: 4.5361 S13: -2.9966 REMARK 3 S21: -1.1109 S22: -0.8180 S23: -1.9965 REMARK 3 S31: 3.3698 S32: 3.4448 S33: -1.2763 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN B AND RESI 118:189 REMARK 3 ORIGIN FOR THE GROUP (A): 21.5015 -3.7653 59.7434 REMARK 3 T TENSOR REMARK 3 T11: 0.3651 T22: 0.3822 REMARK 3 T33: 0.2448 T12: -0.0285 REMARK 3 T13: 0.0552 T23: 0.0345 REMARK 3 L TENSOR REMARK 3 L11: 2.1459 L22: 3.7742 REMARK 3 L33: 7.5595 L12: -0.0152 REMARK 3 L13: -1.9494 L23: -0.0158 REMARK 3 S TENSOR REMARK 3 S11: -0.1501 S12: -0.3357 S13: -0.4907 REMARK 3 S21: -0.0662 S22: 0.0297 S23: 0.1251 REMARK 3 S31: 0.4431 S32: -0.0573 S33: 0.1358 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 4MUT 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_1000082392. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-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-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : C(111) 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 : 20150 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 39.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.57300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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 (%): 45.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MAGNESIUM CHLORIDE, 0.05 M MES, REMARK 280 20% PEG 8K, 2.5 MM ACETYL-L-LYS-D-ALA-D-ALA, PH 5.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 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, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 30.71334 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 2.79315 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -61.38455 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 MET A 1 REMARK 465 PHE A 189 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 MET B 1 REMARK 465 ALA B 190 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 N DAL B 202 O HOH B 444 2.12 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 GLN A 108 97.83 -66.65 REMARK 500 PHE A 118 52.31 -150.98 REMARK 500 PHE B 118 48.37 -151.52 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 204 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 99.1 REMARK 620 3 HIS A 156 ND1 104.8 96.3 REMARK 620 4 HOH A 468 O 80.8 99.0 162.7 REMARK 620 5 HOH A 469 O 159.5 80.5 95.6 79.0 REMARK 620 N 1 2 3 4 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 100.9 REMARK 620 3 HIS B 156 ND1 101.8 98.9 REMARK 620 4 HOH B 443 O 82.0 111.1 148.6 REMARK 620 5 HOH B 444 O 147.4 100.8 98.5 67.5 REMARK 620 N 1 2 3 4 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 DAL 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 PE3 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 203 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: 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: 4F78 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE BIFUNCTIONAL D,D- REMARK 900 DIPEPTIDASE/D,D-CARBOXYPEPTIDASE VANXYG FROM ENTEROCOCCUS FAECALIS 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 4MUT A 1 190 UNP Q9JN36 Q9JN36_ENTGA 1 190 DBREF 4MUT B 1 190 UNP Q9JN36 Q9JN36_ENTGA 1 190 SEQADV 4MUT MET A -20 UNP Q9JN36 INITIATING METHIONINE SEQADV 4MUT GLY A -19 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT SER A -18 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT SER A -17 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS A -16 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS A -15 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS A -14 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS A -13 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS A -12 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS A -11 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT SER A -10 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT SER A -9 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT GLY A -8 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT ARG A -7 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT GLU A -6 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT ASN A -5 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT LEU A -4 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT TYR A -3 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT PHE A -2 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT GLN A -1 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT GLY A 0 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT SER A 59 UNP Q9JN36 ASP 59 ENGINEERED MUTATION SEQADV 4MUT MET B -20 UNP Q9JN36 INITIATING METHIONINE SEQADV 4MUT GLY B -19 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT SER B -18 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT SER B -17 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS B -16 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS B -15 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS B -14 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS B -13 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS B -12 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT HIS B -11 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT SER B -10 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT SER B -9 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT GLY B -8 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT ARG B -7 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT GLU B -6 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT ASN B -5 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT LEU B -4 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT TYR B -3 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT PHE B -2 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT GLN B -1 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT GLY B 0 UNP Q9JN36 EXPRESSION TAG SEQADV 4MUT 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 DAL A 202 6 HET CL A 203 1 HET PE3 A 204 5 HET ZN B 201 1 HET DAL B 202 6 HET SO4 B 203 5 HETNAM ZN ZINC ION HETNAM DAL D-ALANINE 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 DAL 2(C3 H7 N O2) FORMUL 5 CL CL 1- FORMUL 6 PE3 C28 H58 O15 FORMUL 9 SO4 O4 S 2- FORMUL 10 HOH *315(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 LYS A 172 1 10 HELIX 9 9 THR A 174 ARG A 187 1 14 HELIX 10 10 GLN B 35 GLY B 50 1 16 HELIX 11 11 THR B 63 GLY B 79 1 17 HELIX 12 12 GLY B 79 VAL B 87 1 9 HELIX 13 13 SER B 93 GLY B 98 5 6 HELIX 14 14 SER B 121 MET B 131 1 11 HELIX 15 15 MET B 132 TYR B 134 5 3 HELIX 16 16 LYS B 144 GLY B 149 1 6 HELIX 17 17 PRO B 163 LYS B 172 1 10 HELIX 18 18 THR B 174 GLN B 188 1 15 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 GLU A 153 TYR A 159 -1 O PHE A 157 N ILE A 101 SHEET 4 B 4 PHE A 136 TYR A 140 -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 2.24 LINK OD1 ASP A 102 ZN ZN A 201 1555 1555 2.12 LINK ND1 HIS A 156 ZN ZN A 201 1555 1555 2.15 LINK ZN ZN A 201 O HOH A 468 1555 1555 2.13 LINK ZN ZN A 201 O HOH A 469 1555 1555 2.06 LINK NE2 HIS B 95 ZN ZN B 201 1555 1555 2.24 LINK OD1 ASP B 102 ZN ZN B 201 1555 1555 2.09 LINK ND1 HIS B 156 ZN ZN B 201 1555 1555 2.23 LINK ZN ZN B 201 O HOH B 443 1555 1555 2.11 LINK ZN ZN B 201 O HOH B 444 1555 1555 2.08 CISPEP 1 LEU A 162 PRO A 163 0 -2.33 CISPEP 2 LEU B 162 PRO B 163 0 -5.23 SITE 1 AC1 6 HIS A 95 ASP A 102 HIS A 156 DAL A 202 SITE 2 AC1 6 HOH A 468 HOH A 469 SITE 1 AC2 13 GLN A 67 PHE A 86 ALA A 88 SER A 93 SITE 2 AC2 13 HIS A 95 GLU A 153 HIS A 156 ZN A 201 SITE 3 AC2 13 HOH A 406 HOH A 407 HOH A 408 HOH A 468 SITE 4 AC2 13 HOH A 469 SITE 1 AC3 3 HIS A 21 LEU A 22 ARG B 69 SITE 1 AC4 4 ASN A 2 LEU A 6 HIS A 179 PHE B 189 SITE 1 AC5 6 HIS B 95 ASP B 102 HIS B 156 DAL B 202 SITE 2 AC5 6 HOH B 443 HOH B 444 SITE 1 AC6 13 ARG B 62 GLN B 67 PHE B 86 ALA B 88 SITE 2 AC6 13 SER B 93 HIS B 95 TYR B 140 GLU B 153 SITE 3 AC6 13 ZN B 201 HOH B 386 HOH B 443 HOH B 444 SITE 4 AC6 13 HOH B 445 SITE 1 AC7 6 ARG A 119 HOH A 335 LYS B 65 ARG B 68 SITE 2 AC7 6 ARG B 69 HOH B 366 CRYST1 44.674 45.214 63.014 86.69 77.20 63.88 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 0.022384 -0.010976 -0.005590 0.00000 SCALE2 0.000000 0.024633 0.001121 0.00000 SCALE3 0.000000 0.000000 0.016291 0.00000