HEADER HYDROLASE 26-AUG-22 8GPE TITLE CRYSTAL STRUCTURE OF NDM-1 AT PH5.5 (SUCCINATE) IN COMPLEX WITH TITLE 2 HYDROLYZED PENICILLIN G COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO BETA LACTAMASE NDM-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: METALLO BETA-LACTAMASE,METALLO-BETA-LACTAMASE NDM1, COMPND 5 METALLOBETALACTAMASE NDM-1,NDM-1,NDM1 METALLO-BETA-LACTAMASE,NEW COMPND 6 DELHI METALLO CARBAPENEMASE-1,NEW DELHI METALLO-BETA-LACTAMASE NDM-1, COMPND 7 NEW DELHI METALLO-BETA-LACTAMSE 1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLANDM-1, BLA NDM-1, BLANDM1, NDM-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.SHI,Y.DAI,Q.ZHANG,W.LIU REVDAT 2 28-FEB-24 8GPE 1 JRNL REVDAT 1 30-AUG-23 8GPE 0 JRNL AUTH X.SHI,Y.DAI,Z.LAN,S.WANG,L.CUI,C.XIAO,K.ZHAO,X.LI,W.LIU, JRNL AUTH 2 Q.ZHANG JRNL TITL INTERPLAY BETWEEN THE BETA-LACTAM SIDE CHAIN AND AN JRNL TITL 2 ACTIVE-SITE MOBILE LOOP OF NDM-1 IN PENICILLIN HYDROLYSIS AS JRNL TITL 3 A POTENTIAL TARGET FOR MECHANISM-BASED INHIBITOR DESIGN. JRNL REF INT.J.BIOL.MACROMOL. V. 262 30041 2024 JRNL REFN ISSN 0141-8130 JRNL PMID 38336327 JRNL DOI 10.1016/J.IJBIOMAC.2024.130041 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 81075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.160 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4137 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.9300 - 4.3500 1.00 2873 137 0.1547 0.1778 REMARK 3 2 4.3500 - 3.4500 1.00 2729 146 0.1339 0.1400 REMARK 3 3 3.4500 - 3.0200 1.00 2667 146 0.1398 0.1589 REMARK 3 4 3.0200 - 2.7400 1.00 2679 153 0.1398 0.1749 REMARK 3 5 2.7400 - 2.5400 1.00 2660 140 0.1414 0.1468 REMARK 3 6 2.5400 - 2.3900 1.00 2660 134 0.1341 0.1478 REMARK 3 7 2.3900 - 2.2700 1.00 2605 166 0.1295 0.1593 REMARK 3 8 2.2700 - 2.1700 1.00 2618 152 0.1218 0.1537 REMARK 3 9 2.1700 - 2.0900 1.00 2645 136 0.1228 0.1580 REMARK 3 10 2.0900 - 2.0200 1.00 2610 165 0.1274 0.1503 REMARK 3 11 2.0200 - 1.9600 1.00 2602 130 0.1271 0.1504 REMARK 3 12 1.9600 - 1.9000 1.00 2660 143 0.1220 0.1518 REMARK 3 13 1.9000 - 1.8500 1.00 2604 133 0.1190 0.1593 REMARK 3 14 1.8500 - 1.8000 1.00 2619 128 0.1137 0.1599 REMARK 3 15 1.8000 - 1.7600 1.00 2597 148 0.1137 0.1597 REMARK 3 16 1.7600 - 1.7300 1.00 2618 135 0.1164 0.1706 REMARK 3 17 1.7300 - 1.6900 1.00 2601 150 0.1159 0.1546 REMARK 3 18 1.6900 - 1.6600 1.00 2593 141 0.1179 0.1541 REMARK 3 19 1.6600 - 1.6300 1.00 2590 150 0.1248 0.1890 REMARK 3 20 1.6300 - 1.6000 1.00 2630 138 0.1151 0.1533 REMARK 3 21 1.6000 - 1.5800 1.00 2577 134 0.1073 0.1703 REMARK 3 22 1.5800 - 1.5500 1.00 2587 134 0.1039 0.1683 REMARK 3 23 1.5500 - 1.5300 0.99 2625 123 0.1031 0.1463 REMARK 3 24 1.5300 - 1.5100 0.99 2545 142 0.1013 0.1533 REMARK 3 25 1.5100 - 1.4900 0.98 2559 136 0.1070 0.1735 REMARK 3 26 1.4900 - 1.4700 0.95 2457 141 0.1045 0.1509 REMARK 3 27 1.4700 - 1.4500 0.91 2344 116 0.1099 0.1638 REMARK 3 28 1.4500 - 1.4300 0.88 2317 132 0.1197 0.1970 REMARK 3 29 1.4300 - 1.4200 0.82 2116 98 0.1490 0.2270 REMARK 3 30 1.4200 - 1.4000 0.76 1951 110 0.1834 0.2477 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) : 0.111 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.736 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.62 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 : 0.007 3770 REMARK 3 ANGLE : 0.991 5153 REMARK 3 CHIRALITY : 0.089 577 REMARK 3 PLANARITY : 0.009 693 REMARK 3 DIHEDRAL : 6.086 563 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8GPE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031853. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81080 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 38.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.1_4122 REMARK 200 STARTING MODEL: 4RL2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SUCCINATE PH5.5, 32%PEG3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 19.58500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.58000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.06000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.58500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.58000 REMARK 290 SMTRY3 4 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 1 REMARK 465 GLU A 2 REMARK 465 LEU A 3 REMARK 465 PRO A 4 REMARK 465 ASN A 5 REMARK 465 ILE A 6 REMARK 465 MET A 7 REMARK 465 HIS A 8 REMARK 465 PRO A 9 REMARK 465 VAL A 10 REMARK 465 ALA A 11 REMARK 465 LYS A 12 REMARK 465 LEU A 13 REMARK 465 SER A 14 REMARK 465 THR A 15 REMARK 465 ALA A 16 REMARK 465 LEU A 17 REMARK 465 ALA A 18 REMARK 465 ALA A 19 REMARK 465 ALA A 20 REMARK 465 LEU A 21 REMARK 465 MET A 22 REMARK 465 LEU A 23 REMARK 465 SER A 24 REMARK 465 GLY A 25 REMARK 465 CYS A 26 REMARK 465 MET A 27 REMARK 465 PRO A 28 REMARK 465 GLY A 29 REMARK 465 GLU A 30 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 LEU B 3 REMARK 465 PRO B 4 REMARK 465 ASN B 5 REMARK 465 ILE B 6 REMARK 465 MET B 7 REMARK 465 HIS B 8 REMARK 465 PRO B 9 REMARK 465 VAL B 10 REMARK 465 ALA B 11 REMARK 465 LYS B 12 REMARK 465 LEU B 13 REMARK 465 SER B 14 REMARK 465 THR B 15 REMARK 465 ALA B 16 REMARK 465 LEU B 17 REMARK 465 ALA B 18 REMARK 465 ALA B 19 REMARK 465 ALA B 20 REMARK 465 LEU B 21 REMARK 465 MET B 22 REMARK 465 LEU B 23 REMARK 465 SER B 24 REMARK 465 GLY B 25 REMARK 465 CYS B 26 REMARK 465 MET B 27 REMARK 465 PRO B 28 REMARK 465 GLY B 29 REMARK 465 GLU B 30 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 O HOH A 443 O HOH A 515 1.91 REMARK 500 O HOH B 643 O HOH B 672 2.00 REMARK 500 O HOH A 620 O HOH A 634 2.02 REMARK 500 O HOH A 443 O HOH A 668 2.02 REMARK 500 O HOH A 479 O HOH A 613 2.03 REMARK 500 O HOH B 443 O HOH B 621 2.05 REMARK 500 ND2 ASN B 103 O HOH B 401 2.07 REMARK 500 O HOH A 432 O HOH A 630 2.07 REMARK 500 O HOH B 497 O HOH B 625 2.08 REMARK 500 O HOH A 584 O HOH A 606 2.08 REMARK 500 O HOH A 572 O HOH A 592 2.09 REMARK 500 OD1 ASP B 96 O HOH B 402 2.11 REMARK 500 O HOH B 644 O HOH B 667 2.13 REMARK 500 O HOH B 503 O HOH B 601 2.13 REMARK 500 OD1 ASP B 95 O HOH B 403 2.13 REMARK 500 OD1 ASP A 82 O HOH A 401 2.14 REMARK 500 OD1 ASN B 103 O HOH B 404 2.15 REMARK 500 OD1 ASN B 103 O HOH B 405 2.15 REMARK 500 O HOH A 605 O HOH A 632 2.15 REMARK 500 O HOH A 604 O HOH A 657 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 539 O HOH A 558 4455 1.99 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 PHE A 70 -35.79 -137.82 REMARK 500 ASP A 90 143.78 76.37 REMARK 500 ASP B 90 142.55 72.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 730 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 731 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH B 713 DISTANCE = 5.91 ANGSTROMS 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 120 NE2 REMARK 620 2 HIS A 122 ND1 101.4 REMARK 620 3 HIS A 189 NE2 98.5 122.3 REMARK 620 4 PNK A 303 O3 174.0 84.2 79.8 REMARK 620 5 HOH A 420 O 90.7 121.8 111.4 84.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 97.7 REMARK 620 3 HIS A 250 NE2 89.7 112.3 REMARK 620 4 PNK A 303 N1 94.4 132.0 114.0 REMARK 620 5 PNK A 303 O1 166.7 95.3 88.1 74.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 304 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 152 OE1 REMARK 620 2 GLU A 152 OE2 52.2 REMARK 620 3 ASP A 223 OD1 136.1 142.2 REMARK 620 4 ASP A 223 OD2 92.8 103.0 48.6 REMARK 620 5 GLU B 227 OE1 72.5 124.6 80.0 80.6 REMARK 620 6 GLU B 227 OE2 72.6 124.5 81.1 82.5 2.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 101.2 REMARK 620 3 HIS B 189 NE2 100.3 121.4 REMARK 620 4 PNK B 303 O4 174.1 83.7 79.6 REMARK 620 5 HOH B 424 O 91.3 122.2 111.0 83.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 124 OD2 REMARK 620 2 CYS B 208 SG 97.4 REMARK 620 3 HIS B 250 NE2 87.5 113.0 REMARK 620 4 PNK B 303 N1 95.0 132.8 113.0 REMARK 620 5 PNK B 303 O2 165.9 96.7 88.0 74.6 REMARK 620 N 1 2 3 4 DBREF 8GPE A 1 270 UNP E9NWK5 E9NWK5_KLEPN 1 270 DBREF 8GPE B 1 270 UNP E9NWK5 E9NWK5_KLEPN 1 270 SEQRES 1 A 270 MET GLU LEU PRO ASN ILE MET HIS PRO VAL ALA LYS LEU SEQRES 2 A 270 SER THR ALA LEU ALA ALA ALA LEU MET LEU SER GLY CYS SEQRES 3 A 270 MET PRO GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET SEQRES 4 A 270 GLU THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG SEQRES 5 A 270 GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU SEQRES 6 A 270 ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU SEQRES 7 A 270 ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR SEQRES 8 A 270 ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP SEQRES 9 A 270 ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL SEQRES 10 A 270 VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP SEQRES 11 A 270 ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA SEQRES 12 A 270 LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA SEQRES 13 A 270 ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL SEQRES 14 A 270 GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL SEQRES 15 A 270 PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR SEQRES 16 A 270 VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS SEQRES 17 A 270 LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU SEQRES 18 A 270 GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG SEQRES 19 A 270 ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL SEQRES 20 A 270 MET SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR SEQRES 21 A 270 HIS THR ALA ARG MET ALA ASP LYS LEU ARG SEQRES 1 B 270 MET GLU LEU PRO ASN ILE MET HIS PRO VAL ALA LYS LEU SEQRES 2 B 270 SER THR ALA LEU ALA ALA ALA LEU MET LEU SER GLY CYS SEQRES 3 B 270 MET PRO GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET SEQRES 4 B 270 GLU THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG SEQRES 5 B 270 GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU SEQRES 6 B 270 ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU SEQRES 7 B 270 ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR SEQRES 8 B 270 ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP SEQRES 9 B 270 ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL SEQRES 10 B 270 VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP SEQRES 11 B 270 ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA SEQRES 12 B 270 LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA SEQRES 13 B 270 ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL SEQRES 14 B 270 GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL SEQRES 15 B 270 PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR SEQRES 16 B 270 VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS SEQRES 17 B 270 LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU SEQRES 18 B 270 GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG SEQRES 19 B 270 ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL SEQRES 20 B 270 MET SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR SEQRES 21 B 270 HIS THR ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 301 1 HET ZN A 302 1 HET PNK A 303 42 HET K A 304 1 HET ZN B 301 1 HET ZN B 302 1 HET PNK B 303 42 HETNAM ZN ZINC ION HETNAM PNK (2R,4S)-2-{(R)-CARBOXY[(PHENYLACETYL)AMINO]METHYL}-5,5- HETNAM 2 PNK DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID HETNAM K POTASSIUM ION HETSYN PNK PENICILLIN, HYDROXYLATED FORM FORMUL 3 ZN 4(ZN 2+) FORMUL 5 PNK 2(C16 H20 N2 O5 S) FORMUL 6 K K 1+ FORMUL 10 HOH *644(H2 O) HELIX 1 AA1 THR A 94 ILE A 109 1 16 HELIX 2 AA2 HIS A 122 GLY A 127 1 6 HELIX 3 AA3 GLY A 128 ALA A 135 1 8 HELIX 4 AA4 ALA A 143 ALA A 149 1 7 HELIX 5 AA5 PRO A 150 GLY A 153 5 4 HELIX 6 AA6 GLU A 170 ALA A 174 5 5 HELIX 7 AA7 HIS A 228 PHE A 240 1 13 HELIX 8 AA8 ARG A 256 LYS A 268 1 13 HELIX 9 AA9 THR B 94 ILE B 109 1 16 HELIX 10 AB1 HIS B 122 GLY B 127 1 6 HELIX 11 AB2 GLY B 128 ALA B 135 1 8 HELIX 12 AB3 ALA B 143 ALA B 149 1 7 HELIX 13 AB4 PRO B 150 GLY B 153 5 4 HELIX 14 AB5 GLU B 170 ALA B 174 5 5 HELIX 15 AB6 HIS B 228 PHE B 240 1 13 HELIX 16 AB7 ARG B 256 LYS B 268 1 13 SHEET 1 AA1 8 ASP A 43 PHE A 46 0 SHEET 2 AA1 8 LEU A 49 ALA A 55 -1 O PHE A 51 N GLN A 44 SHEET 3 AA1 8 VAL A 58 MET A 67 -1 O GLN A 60 N ARG A 52 SHEET 4 AA1 8 GLY A 71 ASP A 82 -1 O GLY A 71 N MET A 67 SHEET 5 AA1 8 ARG A 85 VAL A 89 -1 O LEU A 87 N VAL A 80 SHEET 6 AA1 8 VAL A 113 VAL A 117 1 O VAL A 117 N VAL A 88 SHEET 7 AA1 8 ALA A 138 ASN A 142 1 O TYR A 140 N ALA A 116 SHEET 8 AA1 8 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141 SHEET 1 AA2 4 LEU A 180 PHE A 183 0 SHEET 2 AA2 4 THR A 195 ILE A 198 -1 O GLY A 197 N LYS A 181 SHEET 3 AA2 4 ILE A 203 PHE A 205 -1 O PHE A 205 N VAL A 196 SHEET 4 AA2 4 MET A 245 VAL A 247 1 O VAL A 247 N ALA A 204 SHEET 1 AA3 8 ASP B 43 PHE B 46 0 SHEET 2 AA3 8 LEU B 49 ALA B 55 -1 O PHE B 51 N GLN B 44 SHEET 3 AA3 8 VAL B 58 MET B 67 -1 O GLN B 60 N ARG B 52 SHEET 4 AA3 8 GLY B 71 ASP B 82 -1 O ILE B 79 N TRP B 59 SHEET 5 AA3 8 ARG B 85 VAL B 89 -1 O ARG B 85 N ASP B 82 SHEET 6 AA3 8 VAL B 113 VAL B 117 1 O ALA B 114 N VAL B 86 SHEET 7 AA3 8 ALA B 138 ASN B 142 1 O TYR B 140 N ALA B 116 SHEET 8 AA3 8 HIS B 159 LEU B 161 1 O LEU B 161 N ALA B 141 SHEET 1 AA4 4 LEU B 180 PHE B 183 0 SHEET 2 AA4 4 THR B 195 ILE B 198 -1 O GLY B 197 N LYS B 181 SHEET 3 AA4 4 ILE B 203 PHE B 205 -1 O PHE B 205 N VAL B 196 SHEET 4 AA4 4 MET B 245 VAL B 247 1 O VAL B 247 N ALA B 204 LINK NE2 HIS A 120 ZN ZN A 301 1555 1555 2.16 LINK ND1 HIS A 122 ZN ZN A 301 1555 1555 2.09 LINK OD2 ASP A 124 ZN ZN A 302 1555 1555 2.11 LINK OE1 GLU A 152 K K A 304 1555 1555 2.62 LINK OE2 GLU A 152 K K A 304 1555 1555 2.22 LINK NE2 HIS A 189 ZN ZN A 301 1555 1555 2.10 LINK SG CYS A 208 ZN ZN A 302 1555 1555 2.34 LINK OD1 ASP A 223 K K A 304 1555 1555 2.93 LINK OD2 ASP A 223 K K A 304 1555 1555 2.12 LINK NE2 HIS A 250 ZN ZN A 302 1555 1555 2.10 LINK ZN ZN A 301 O3 PNK A 303 1555 1555 2.50 LINK ZN ZN A 301 O HOH A 420 1555 1555 1.84 LINK ZN ZN A 302 N1 PNK A 303 1555 1555 2.18 LINK ZN ZN A 302 O1 PNK A 303 1555 1555 2.18 LINK K K A 304 OE1 GLU B 227 3444 1555 2.65 LINK K K A 304 OE2 GLU B 227 3444 1555 2.20 LINK NE2 HIS B 120 ZN ZN B 301 1555 1555 2.16 LINK ND1 HIS B 122 ZN ZN B 301 1555 1555 2.13 LINK OD2 ASP B 124 ZN ZN B 302 1555 1555 2.15 LINK NE2 HIS B 189 ZN ZN B 301 1555 1555 2.11 LINK SG CYS B 208 ZN ZN B 302 1555 1555 2.34 LINK NE2 HIS B 250 ZN ZN B 302 1555 1555 2.10 LINK ZN ZN B 301 O4 PNK B 303 1555 1555 2.51 LINK ZN ZN B 301 O HOH B 424 1555 1555 1.85 LINK ZN ZN B 302 N1 PNK B 303 1555 1555 2.16 LINK ZN ZN B 302 O2 PNK B 303 1555 1555 2.20 CRYST1 39.170 79.160 134.120 90.00 90.00 90.00 P 21 21 21 8 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 0.025530 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007456 0.00000