HEADER HYDROLASE/ANTIBIOTIC 03-FEB-17 5N0H TITLE CRYSTAL STRUCTURE OF NDM-1 IN COMPLEX WITH HYDROLYZED MEROPENEM - 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 BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS HYDROLASE-ANTIBIOTIC COMPLEX, METALLO-BETA-LACTAMASE, NDM-1 EXPDTA X-RAY DIFFRACTION AUTHOR J.E.RACZYNSKA,I.G.SHABALIN,M.JASKOLSKI,W.MINOR,A.WLODAWER,D.T.KING, AUTHOR 2 N.C.J.STRYNADKA REVDAT 5 08-MAY-24 5N0H 1 COMPND HETNAM LINK REVDAT 4 16-OCT-19 5N0H 1 REMARK REVDAT 3 26-DEC-18 5N0H 1 JRNL REVDAT 2 13-DEC-17 5N0H 1 CAVEAT COMPND REMARK HET REVDAT 2 2 1 HETNAM HETSYN FORMUL LINK REVDAT 2 3 1 SITE ATOM REVDAT 1 05-APR-17 5N0H 0 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 0 REMARK 0 THIS ENTRY 5N0I REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 STRUCTURAL DATA (R4EYLSF) DETERMINED BY AUTHORS OF THE PDB ENTRY REMARK 0 4EYL: D.T.KING, N.C.J.STRYNADKA ORIGINAL DATA REFERENCE 1 PDB ID: REMARK 0 4EYL AUTH D.T.KING,L.J.WORRALL,R.GRUNINGER,N.C.STRYNADKA TITL REMARK 0 NEW DELHI METALLO-BETA-LACTAMASE: STRUCTURAL INSIGHTS INTO TITL REMARK 0 2 BETA-LACTAM RECOGNITION AND INHIBITION REF J.AM.CHEM.SOC. V. REMARK 0 134 11362 2012 REFN ISSN 0002-7863 PMID 22713171 DOI 10.1021/ REMARK 0 JA303579D REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 38308 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : COPIED FROM 4EYL REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2030 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2626 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3510 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 398 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.09000 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): 0.128 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.127 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3677 ; 0.044 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3454 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4979 ; 1.797 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7915 ; 4.256 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 473 ; 6.416 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;34.478 ;24.539 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 541 ;13.398 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.595 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 565 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4223 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 835 ; 0.054 ; 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): 1895 ; 1.812 ; 1.769 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1894 ; 1.803 ; 1.768 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2364 ; 2.809 ; 2.638 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2365 ; 2.809 ; 2.639 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1782 ; 2.639 ; 2.072 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1778 ; 2.638 ; 2.069 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2609 ; 4.087 ; 2.967 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4287 ; 6.692 ;15.537 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4287 ; 6.692 ;15.536 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): NULL ; NULL ; NULL 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 5N0H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : TOROIDAL FOCUSING MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40390 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 999.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 999.0000 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M TRISODIUM CACODYLATE, 0.1M SODIUM REMARK 280 CACODYLATE , PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.29000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.14500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.43500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.14500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.43500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 46.29000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 29 REMARK 465 GLU A 30 REMARK 465 ILE A 31 REMARK 465 ARG A 32 REMARK 465 PRO A 33 REMARK 465 THR A 34 REMARK 465 ILE A 35 REMARK 465 GLY A 36 REMARK 465 GLN A 37 REMARK 465 GLN A 38 REMARK 465 MET A 39 REMARK 465 GLU A 40 REMARK 465 GLY B 29 REMARK 465 GLU B 30 REMARK 465 ILE B 31 REMARK 465 ARG B 32 REMARK 465 UNK B 273 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 70 CG CD1 CD2 CE1 CE2 CZ 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 B 528 O HOH B 542 2.08 REMARK 500 O HOH A 491 O HOH A 499 2.09 REMARK 500 OG SER A 251 O HOH A 401 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 66 73.42 -114.54 REMARK 500 ASP A 82 75.83 -104.10 REMARK 500 ASP A 90 146.84 70.28 REMARK 500 ASP B 90 143.69 77.24 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 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 102.7 REMARK 620 3 HIS A 189 NE2 103.1 114.3 REMARK 620 4 8YL A 301 OAF 133.4 105.5 98.2 REMARK 620 5 HOH A 535 O 122.6 105.0 109.5 12.8 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 102.6 REMARK 620 3 HIS A 250 NE2 93.8 108.1 REMARK 620 4 8YL A 301 OAF 99.9 103.0 142.3 REMARK 620 5 8YL A 301 NAN 96.0 154.2 88.2 55.7 REMARK 620 6 8YL A 301 OAH 165.0 87.6 72.4 88.3 78.2 REMARK 620 7 HOH A 535 O 89.5 104.0 146.2 10.5 58.0 98.8 REMARK 620 N 1 2 3 4 5 6 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 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 101.5 REMARK 620 3 HIS B 189 NE2 105.8 113.3 REMARK 620 4 HOH B 542 O 120.1 113.3 103.1 REMARK 620 N 1 2 3 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 ASP B 124 OD2 REMARK 620 2 CYS B 208 SG 104.8 REMARK 620 3 HIS B 250 NE2 94.0 111.1 REMARK 620 4 HOH B 542 O 94.3 102.5 141.9 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 8YL 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 ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL 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 ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EYL RELATED DB: PDB DBREF 5N0H A 29 270 UNP C7C422 BLAN1_KLEPN 29 270 DBREF 5N0H B 29 270 UNP C7C422 BLAN1_KLEPN 29 270 SEQADV 5N0H LYS A 271 UNP C7C422 EXPRESSION TAG SEQADV 5N0H LEU A 272 UNP C7C422 EXPRESSION TAG SEQADV 5N0H UNK A 273 UNP C7C422 EXPRESSION TAG SEQADV 5N0H LYS B 271 UNP C7C422 EXPRESSION TAG SEQADV 5N0H LEU B 272 UNP C7C422 EXPRESSION TAG SEQADV 5N0H UNK B 273 UNP C7C422 EXPRESSION TAG SEQRES 1 A 245 GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU THR SEQRES 2 A 245 GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU SEQRES 3 A 245 ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET SEQRES 4 A 245 PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL SEQRES 5 A 245 ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP SEQRES 6 A 245 THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS SEQRES 7 A 245 GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR SEQRES 8 A 245 HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU SEQRES 9 A 245 HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER SEQRES 10 A 245 ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN SEQRES 11 A 245 HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO SEQRES 12 A 245 ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR SEQRES 13 A 245 PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY SEQRES 14 A 245 ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE SEQRES 15 A 245 LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP SEQRES 16 A 245 ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE SEQRES 17 A 245 GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER SEQRES 18 A 245 HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR SEQRES 19 A 245 ALA ARG MET ALA ASP LYS LEU ARG LYS LEU UNK SEQRES 1 B 245 GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU THR SEQRES 2 B 245 GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU SEQRES 3 B 245 ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET SEQRES 4 B 245 PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL SEQRES 5 B 245 ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP SEQRES 6 B 245 THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS SEQRES 7 B 245 GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR SEQRES 8 B 245 HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU SEQRES 9 B 245 HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER SEQRES 10 B 245 ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN SEQRES 11 B 245 HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO SEQRES 12 B 245 ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR SEQRES 13 B 245 PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY SEQRES 14 B 245 ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE SEQRES 15 B 245 LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP SEQRES 16 B 245 ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE SEQRES 17 B 245 GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER SEQRES 18 B 245 HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR SEQRES 19 B 245 ALA ARG MET ALA ASP LYS LEU ARG LYS LEU UNK HET 8YL A 301 27 HET ZN A 302 1 HET ZN A 303 1 HET GOL A 304 6 HET GOL A 305 6 HET SO4 A 306 5 HET ZN B 301 1 HET ZN B 302 1 HET GOL B 303 6 HET GOL B 304 6 HET GOL B 305 6 HETNAM 8YL (2S,3R)-2-[(2S,3R)-1,3-BIS(OXIDANYL)-1-OXIDANYLIDENE- HETNAM 2 8YL BUTAN-2-YL]-4-[(3S,5S)-5-(DIMETHYLCARBAMOYL) HETNAM 3 8YL PYRROLIDIN-3-YL]SULFAN YL-3-METHYL-2,3-DIHYDRO-1H- HETNAM 4 8YL PYRROLE-5-CARBOXYLIC ACID HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN 8YL MEROPENEM, HYDROLYZED FORM HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 8YL C17 H27 N3 O6 S FORMUL 4 ZN 4(ZN 2+) FORMUL 6 GOL 5(C3 H8 O3) FORMUL 8 SO4 O4 S 2- FORMUL 14 HOH *398(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 LEU A 272 1 17 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 GLY B 153 1 11 HELIX 12 AB3 GLU B 170 ALA B 174 5 5 HELIX 13 AB4 HIS B 228 PHE B 240 1 13 HELIX 14 AB5 ARG B 256 LYS B 271 1 16 SHEET 1 AA1 8 ASP A 43 PHE A 46 0 SHEET 2 AA1 8 LEU A 49 ALA A 55 -1 O LEU A 49 N PHE A 46 SHEET 3 AA1 8 VAL A 58 LEU A 65 -1 O VAL A 58 N LEU A 54 SHEET 4 AA1 8 VAL A 73 ASP A 82 -1 O ILE A 79 N TRP A 59 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 118 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 THR A 195 N PHE A 183 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 9 GLN B 37 GLN B 38 0 SHEET 2 AA3 9 GLN B 44 PHE B 46 -1 O ARG B 45 N GLN B 37 SHEET 3 AA3 9 LEU B 49 ALA B 55 -1 O LEU B 49 N PHE B 46 SHEET 4 AA3 9 VAL B 58 TYR B 64 -1 O GLN B 60 N ARG B 52 SHEET 5 AA3 9 ALA B 74 ASP B 82 -1 O ILE B 79 N TRP B 59 SHEET 6 AA3 9 ARG B 85 VAL B 89 -1 O LEU B 87 N VAL B 80 SHEET 7 AA3 9 VAL B 113 VAL B 117 1 O VAL B 117 N VAL B 88 SHEET 8 AA3 9 ALA B 138 ASN B 142 1 O TYR B 140 N ALA B 116 SHEET 9 AA3 9 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 THR B 195 N PHE B 183 SHEET 3 AA4 4 ILE B 203 GLY B 207 -1 O PHE B 205 N VAL B 196 SHEET 4 AA4 4 MET B 245 MET B 248 1 O VAL B 247 N GLY B 206 LINK NE2 HIS A 120 ZN ZN A 303 1555 1555 2.06 LINK ND1 HIS A 122 ZN ZN A 303 1555 1555 2.04 LINK OD2 ASP A 124 ZN ZN A 302 1555 1555 2.19 LINK NE2 HIS A 189 ZN ZN A 303 1555 1555 2.07 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 OAFA8YL A 301 ZN ZN A 302 1555 1555 2.66 LINK NANA8YL A 301 ZN ZN A 302 1555 1555 2.07 LINK OAHA8YL A 301 ZN ZN A 302 1555 1555 2.23 LINK OAFA8YL A 301 ZN ZN A 303 1555 1555 2.04 LINK ZN ZN A 302 O BHOH A 535 1555 1555 2.54 LINK ZN ZN A 303 O BHOH A 535 1555 1555 2.18 LINK NE2 HIS B 120 ZN ZN B 302 1555 1555 2.05 LINK ND1 HIS B 122 ZN ZN B 302 1555 1555 2.05 LINK OD2 ASP B 124 ZN ZN B 301 1555 1555 2.15 LINK NE2 HIS B 189 ZN ZN B 302 1555 1555 2.09 LINK SG CYS B 208 ZN ZN B 301 1555 1555 2.33 LINK NE2 HIS B 250 ZN ZN B 301 1555 1555 2.02 LINK ZN ZN B 301 O HOH B 542 1555 1555 2.15 LINK ZN ZN B 302 O HOH B 542 1555 1555 2.08 SITE 1 AC1 14 VAL A 73 HIS A 122 ASP A 124 HIS A 189 SITE 2 AC1 14 CYS A 208 LYS A 211 ASN A 220 HIS A 250 SITE 3 AC1 14 ZN A 302 ZN A 303 HOH A 441 HOH A 535 SITE 4 AC1 14 HOH A 558 HOH A 592 SITE 1 AC2 5 ASP A 124 CYS A 208 HIS A 250 8YL A 301 SITE 2 AC2 5 HOH A 535 SITE 1 AC3 5 HIS A 120 HIS A 122 HIS A 189 8YL A 301 SITE 2 AC3 5 HOH A 535 SITE 1 AC4 5 ARG A 234 ALA A 263 ARG A 264 HOH A 406 SITE 2 AC4 5 HOH A 423 SITE 1 AC5 9 GLY A 197 ILE A 198 THR A 201 ASP A 202 SITE 2 AC5 9 ILE A 203 PHE A 240 LYS A 242 ALA A 243 SITE 3 AC5 9 HOH A 528 SITE 1 AC6 8 ILE A 109 ASN A 110 HOH A 403 GLY B 42 SITE 2 AC6 8 ARG B 52 GLN B 53 GOL B 303 HOH B 515 SITE 1 AC7 5 ASP B 124 CYS B 208 HIS B 250 HOH B 534 SITE 2 AC7 5 HOH B 542 SITE 1 AC8 5 HIS B 120 HIS B 122 HIS B 189 HOH B 528 SITE 2 AC8 5 HOH B 542 SITE 1 AC9 7 ARG A 81 ILE A 109 SO4 A 306 HOH A 471 SITE 2 AC9 7 ARG B 52 LEU B 54 HOH B 405 SITE 1 AD1 5 ILE B 198 THR B 201 ILE B 203 LYS B 242 SITE 2 AD1 5 ALA B 243 SITE 1 AD2 2 GLN B 53 TRP B 59 CRYST1 106.000 106.000 92.580 90.00 90.00 90.00 P 41 21 2 16 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 0.009434 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010801 0.00000