HEADER HYDROLASE 20-MAY-17 5O2F TITLE CRYSTAL STRUCTURE OF NDM-1 IN COMPLEX WITH HYDROLYZED AMPICILLIN - NEW TITLE 2 REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE TYPE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: B2 METALLO-BETA-LACTAMASE,BETA-LACTAMASE TYPE II,METALLO- COMPND 5 BETA-LACTAMASE NDM-1,METALLO-BETA-LACTAMASE TYPE II,NEW DELHI COMPND 6 METALLO-BETA-LACTAMASE-1,NDM-1; COMPND 7 EC: 3.5.2.6; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLANDM-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, NDM-1, METALLO-BETA-LACTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR J.E.RACZYNSKA,I.G.SHABALIN,M.JASKOLSKI,W.MINOR,A.WLODAWER REVDAT 4 07-FEB-24 5O2F 1 REMARK REVDAT 3 02-NOV-22 5O2F 1 REMARK LINK REVDAT 2 16-OCT-19 5O2F 1 SPRSDE REMARK REVDAT 1 26-DEC-18 5O2F 0 SPRSDE 16-OCT-19 5O2F 4RL2 JRNL AUTH J.E.RACZYNSKA,I.G.SHABALIN,W.MINOR,A.WLODAWER,M.JASKOLSKI JRNL TITL A CLOSE LOOK ONTO STRUCTURAL MODELS AND PRIMARY LIGANDS OF JRNL TITL 2 METALLO-BETA-LACTAMASES. JRNL REF DRUG RESIST. UPDAT. V. 40 1 2018 JRNL REFN ESSN 1532-2084 JRNL PMID 30466711 JRNL DOI 10.1016/J.DRUP.2018.08.001 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.FENG,J.DING,D.ZHU,X.LIU,X.XU,Y.ZHANG,S.ZANG,D.C.WANG,W.LIU REMARK 1 TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO NDM-1 CATALYZED REMARK 1 TITL 2 HYDROLYSIS OF CEPHALOSPORINS. REMARK 1 REF J. AM. CHEM. SOC. V. 136 14694 2014 REMARK 1 REFN ESSN 1520-5126 REMARK 1 PMID 25268575 REMARK 1 DOI 10.1021/JA508388E REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 25437 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1345 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1775 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.1460 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.1880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3620 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 87 REMARK 3 SOLVENT ATOMS : 433 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.90000 REMARK 3 B22 (A**2) : -1.52000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.187 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.152 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.774 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3828 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3570 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5209 ; 1.453 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8180 ; 0.959 ; 3.005 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 494 ; 6.204 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;33.418 ;24.534 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 568 ;13.195 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.261 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 581 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4417 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 873 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1952 ; 1.544 ; 1.766 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1951 ; 1.541 ; 1.765 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2439 ; 2.219 ; 2.638 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2440 ; 2.221 ; 2.640 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1876 ; 2.636 ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1876 ; 2.633 ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2766 ; 4.075 ; 8.150 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4472 ; 5.857 ;15.694 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4473 ; 5.858 ;15.699 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4 ; 5.272 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5O2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200005065. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26843 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.008 REMARK 200 RESOLUTION RANGE LOW (A) : 38.785 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: PHASES REMARK 200 STARTING MODEL: 3Q6X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% (W/V) PEG3350, 0.1 M BIS-TRIS, PH REMARK 280 5.8 AND 0.2 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295.0K 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 19.31000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.15500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.78500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.15500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.31000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.78500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 GLY A 25 REMARK 465 SER A 26 REMARK 465 HIS A 27 REMARK 465 GLY B 25 REMARK 465 SER B 26 REMARK 465 HIS B 27 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 OE1 GLN A 151 O HOH A 401 1.98 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 -38.25 -134.68 REMARK 500 ASP A 90 144.83 73.39 REMARK 500 ASP B 90 145.07 75.89 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 120 NE2 REMARK 620 2 HIS A 122 ND1 100.3 REMARK 620 3 HIS A 189 NE2 97.5 125.8 REMARK 620 4 ZZ7 A 303 OXT 177.7 80.9 83.4 REMARK 620 5 HOH A 443 O 92.8 120.7 108.9 84.9 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 94.7 REMARK 620 3 HIS A 250 NE2 92.7 112.6 REMARK 620 4 ZZ7 A 303 O2 168.6 96.0 86.8 REMARK 620 5 ZZ7 A 303 N3 95.4 131.3 114.3 74.5 REMARK 620 N 1 2 3 4 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 101.3 REMARK 620 3 HIS B 189 NE2 101.6 126.8 REMARK 620 4 ZZ7 B 303 O4 170.2 84.3 80.9 REMARK 620 5 HOH B 423 O 92.0 120.7 105.7 78.2 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 96.3 REMARK 620 3 HIS B 250 NE2 90.4 109.2 REMARK 620 4 ZZ7 B 303 N3 95.0 132.8 116.4 REMARK 620 5 ZZ7 B 303 O1 166.6 97.0 87.2 74.4 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZZ7 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZZ7 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RL2 RELATED DB: PDB REMARK 900 RE-REFINEMENT OF ENTRY 4RL2 DBREF 5O2F A 29 270 UNP C7C422 BLAN1_KLEPN 29 270 DBREF 5O2F B 29 270 UNP C7C422 BLAN1_KLEPN 29 270 SEQADV 5O2F GLY A 25 UNP C7C422 EXPRESSION TAG SEQADV 5O2F SER A 26 UNP C7C422 EXPRESSION TAG SEQADV 5O2F HIS A 27 UNP C7C422 EXPRESSION TAG SEQADV 5O2F MET A 28 UNP C7C422 EXPRESSION TAG SEQADV 5O2F GLY B 25 UNP C7C422 EXPRESSION TAG SEQADV 5O2F SER B 26 UNP C7C422 EXPRESSION TAG SEQADV 5O2F HIS B 27 UNP C7C422 EXPRESSION TAG SEQADV 5O2F MET B 28 UNP C7C422 EXPRESSION TAG SEQRES 1 A 246 GLY SER HIS MET GLY GLU ILE ARG PRO THR ILE GLY GLN SEQRES 2 A 246 GLN MET GLU THR GLY ASP GLN ARG PHE GLY ASP LEU VAL SEQRES 3 A 246 PHE ARG GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER SEQRES 4 A 246 TYR LEU ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN SEQRES 5 A 246 GLY LEU ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL SEQRES 6 A 246 ASP THR ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU SEQRES 7 A 246 ASN TRP ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU SEQRES 8 A 246 ALA VAL VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY SEQRES 9 A 246 MET ASP ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA SEQRES 10 A 246 ASN ALA LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET SEQRES 11 A 246 VAL ALA ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY SEQRES 12 A 246 TRP VAL GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU SEQRES 13 A 246 LYS VAL PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN SEQRES 14 A 246 ILE THR VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY SEQRES 15 A 246 GLY CYS LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY SEQRES 16 A 246 ASN LEU GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER SEQRES 17 A 246 ALA ARG ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET SEQRES 18 A 246 ILE VAL MET SER HIS SER ALA PRO ASP SER ARG ALA ALA SEQRES 19 A 246 ILE THR HIS THR ALA ARG MET ALA ASP LYS LEU ARG SEQRES 1 B 246 GLY SER HIS MET GLY GLU ILE ARG PRO THR ILE GLY GLN SEQRES 2 B 246 GLN MET GLU THR GLY ASP GLN ARG PHE GLY ASP LEU VAL SEQRES 3 B 246 PHE ARG GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER SEQRES 4 B 246 TYR LEU ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN SEQRES 5 B 246 GLY LEU ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL SEQRES 6 B 246 ASP THR ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU SEQRES 7 B 246 ASN TRP ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU SEQRES 8 B 246 ALA VAL VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY SEQRES 9 B 246 MET ASP ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA SEQRES 10 B 246 ASN ALA LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET SEQRES 11 B 246 VAL ALA ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY SEQRES 12 B 246 TRP VAL GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU SEQRES 13 B 246 LYS VAL PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN SEQRES 14 B 246 ILE THR VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY SEQRES 15 B 246 GLY CYS LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY SEQRES 16 B 246 ASN LEU GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER SEQRES 17 B 246 ALA ARG ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET SEQRES 18 B 246 ILE VAL MET SER HIS SER ALA PRO ASP SER ARG ALA ALA SEQRES 19 B 246 ILE THR HIS THR ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 301 1 HET ZN A 302 1 HET ZZ7 A 303 25 HET SO4 A 304 5 HET SO4 A 305 5 HET SO4 A 306 5 HET CL A 307 1 HET EDO A 308 4 HET EDO A 309 4 HET ZN B 301 1 HET ZN B 302 1 HET ZZ7 B 303 25 HET SO4 B 304 5 HET EDO B 305 4 HETNAM ZN ZINC ION HETNAM ZZ7 (2R,4S)-2-[(R)-{[(2R)-2-AMINO-2- HETNAM 2 ZZ7 PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3- HETNAM 3 ZZ7 THIAZOLIDINE-4-CARBOXYLIC ACID HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN ZZ7 AMPICILLIN (OPEN FORM) HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 4(ZN 2+) FORMUL 5 ZZ7 2(C16 H21 N3 O5 S) FORMUL 6 SO4 4(O4 S 2-) FORMUL 9 CL CL 1- FORMUL 10 EDO 3(C2 H6 O2) FORMUL 17 HOH *433(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 GLY A 153 1 11 HELIX 5 AA5 GLU A 170 ALA A 174 5 5 HELIX 6 AA6 HIS A 228 PHE A 240 1 13 HELIX 7 AA7 ARG A 256 LYS A 268 1 13 HELIX 8 AA8 THR B 94 ILE B 109 1 16 HELIX 9 AA9 HIS B 122 GLY B 127 1 6 HELIX 10 AB1 GLY B 128 ALA B 135 1 8 HELIX 11 AB2 ALA B 143 ALA B 149 1 7 HELIX 12 AB3 PRO B 150 GLY B 153 5 4 HELIX 13 AB4 GLU B 170 ALA B 174 5 5 HELIX 14 AB5 HIS B 228 PHE B 240 1 13 HELIX 15 AB6 ARG B 256 LYS B 268 1 13 SHEET 1 AA1 8 GLN A 44 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 ILE A 79 N TRP A 59 SHEET 5 AA1 8 ARG A 85 VAL A 89 -1 O VAL A 89 N LEU A 78 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 GLN B 44 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 VAL B 58 N LEU B 54 SHEET 4 AA3 8 GLY B 71 ASP B 82 -1 O SER B 75 N SER B 63 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 2.08 LINK ND1 HIS A 122 ZN ZN A 301 1555 1555 1.98 LINK OD2 ASP A 124 ZN ZN A 302 1555 1555 2.05 LINK NE2 HIS A 189 ZN ZN A 301 1555 1555 2.05 LINK SG CYS A 208 ZN ZN A 302 1555 1555 2.32 LINK NE2 HIS A 250 ZN ZN A 302 1555 1555 2.06 LINK ZN ZN A 301 OXT ZZ7 A 303 1555 1555 2.41 LINK ZN ZN A 301 O HOH A 443 1555 1555 2.00 LINK ZN ZN A 302 O2 ZZ7 A 303 1555 1555 2.18 LINK ZN ZN A 302 N3 ZZ7 A 303 1555 1555 2.17 LINK NE2 HIS B 120 ZN ZN B 301 1555 1555 2.12 LINK ND1 HIS B 122 ZN ZN B 301 1555 1555 2.02 LINK OD2 ASP B 124 ZN ZN B 302 1555 1555 2.04 LINK NE2 HIS B 189 ZN ZN B 301 1555 1555 2.09 LINK SG CYS B 208 ZN ZN B 302 1555 1555 2.34 LINK NE2 HIS B 250 ZN ZN B 302 1555 1555 2.04 LINK ZN ZN B 301 O4 ZZ7 B 303 1555 1555 2.39 LINK ZN ZN B 301 O HOH B 423 1555 1555 1.99 LINK ZN ZN B 302 N3 ZZ7 B 303 1555 1555 2.17 LINK ZN ZN B 302 O1 ZZ7 B 303 1555 1555 2.18 SITE 1 AC1 5 HIS A 120 HIS A 122 HIS A 189 ZZ7 A 303 SITE 2 AC1 5 HOH A 443 SITE 1 AC2 5 ASP A 124 CYS A 208 HIS A 250 ZZ7 A 303 SITE 2 AC2 5 HOH A 443 SITE 1 AC3 20 TRP A 93 HIS A 122 GLN A 123 ASP A 124 SITE 2 AC3 20 HIS A 189 CYS A 208 LYS A 211 GLY A 219 SITE 3 AC3 20 ASN A 220 HIS A 250 ZN A 301 ZN A 302 SITE 4 AC3 20 HOH A 443 HOH A 488 HOH A 491 HOH A 511 SITE 5 AC3 20 THR B 34 PRO B 68 GLY B 69 PHE B 70 SITE 1 AC4 2 ARG A 234 ARG A 264 SITE 1 AC5 3 HIS A 261 ARG A 264 HOH A 481 SITE 1 AC6 5 ARG A 270 HOH A 486 ARG B 264 LYS B 268 SITE 2 AC6 5 HOH B 401 SITE 1 AC7 1 GLY A 29 SITE 1 AC8 5 LYS A 216 SER A 217 HOH A 472 HOH A 514 SITE 2 AC8 5 LYS B 216 SITE 1 AC9 3 HIS A 159 SER A 160 GLY A 178 SITE 1 AD1 5 HIS B 120 HIS B 122 HIS B 189 ZZ7 B 303 SITE 2 AD1 5 HOH B 423 SITE 1 AD2 5 ASP B 124 CYS B 208 HIS B 250 ZZ7 B 303 SITE 2 AD2 5 HOH B 423 SITE 1 AD3 20 THR A 34 PRO A 68 GLY A 69 LEU B 65 SITE 2 AD3 20 TRP B 93 HIS B 122 GLN B 123 ASP B 124 SITE 3 AD3 20 HIS B 189 CYS B 208 LYS B 211 GLY B 219 SITE 4 AD3 20 ASN B 220 HIS B 250 ZN B 301 ZN B 302 SITE 5 AD3 20 HOH B 423 HOH B 505 HOH B 507 HOH B 535 SITE 1 AD4 8 PRO B 150 GLY B 153 HIS B 261 ARG B 264 SITE 2 AD4 8 HOH B 406 HOH B 427 HOH B 490 HOH B 491 SITE 1 AD5 2 HIS B 159 SER B 160 CRYST1 38.620 77.570 132.310 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 0.025893 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012892 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007558 0.00000