HEADER HYDROLASE/ANTIBIOTIC 01-MAY-12 4EYL TITLE CRYSTAL STRUCTURE OF NDM-1 BOUND TO HYDROLYZED MEROPENEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE NDM-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NDM-1, METALLO-BETA-LACTAMASE NDM-1; COMPND 5 EC: 3.5.2.6; COMPND 6 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 METALLO-BETA-LACTAMASE, ANTIBIOTIC, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.C.J.STRYNADKA,D.T.KING REVDAT 4 28-FEB-24 4EYL 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK REVDAT 3 15-NOV-17 4EYL 1 REMARK REVDAT 2 15-AUG-12 4EYL 1 TITLE REVDAT 1 08-AUG-12 4EYL 0 JRNL AUTH D.T.KING,L.J.WORRALL,R.GRUNINGER,N.C.STRYNADKA JRNL TITL NEW DELHI METALLO-BETA-LACTAMASE: STRUCTURAL INSIGHTS INTO JRNL TITL 2 BETA-LACTAM RECOGNITION AND INHIBITION JRNL REF J.AM.CHEM.SOC. V. 134 11362 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22713171 JRNL DOI 10.1021/JA303579D REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD 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 : 38311 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.224 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) : 2628 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3500 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 161 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.28000 REMARK 3 B22 (A**2) : 0.28000 REMARK 3 B33 (A**2) : -0.57000 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): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 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 : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3638 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4961 ; 1.977 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 469 ; 7.638 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;33.826 ;24.510 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 531 ;14.474 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.110 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 562 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2798 ; 0.019 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2332 ; 1.888 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3710 ; 2.845 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1306 ; 4.453 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1251 ; 6.419 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4EYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072231. 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) : 1.00 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 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 : 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 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 298K 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 300 REMARK: IT IS UNCLEAR WHETHER THE BIOLOGICALLY ACTIVE FORM IS REMARK 300 MONOMERIC OR DIMERIC 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 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 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 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 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 THR A 41 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 465 ILE B 31 REMARK 465 ARG B 32 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 OG SER A 251 O HOH A 461 1.95 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 82 72.50 -103.91 REMARK 500 ASP A 90 140.43 77.11 REMARK 500 PRO B 68 118.59 -28.05 REMARK 500 ASP B 90 139.99 76.13 REMARK 500 ASN B 142 133.85 -38.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 66 MET A 67 149.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 85 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 HYDROLYSIS OF MEROPENEM BY BETA-LACTAMASE NDM-1 OCCURRED DURING REMARK 600 CRYSTALLIZATION 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 104.5 REMARK 620 3 HIS A 189 NE2 103.0 113.8 REMARK 620 4 0RV A 301 OAI 124.4 107.9 103.5 REMARK 620 N 1 2 3 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 102.7 REMARK 620 3 HIS A 250 NE2 94.0 110.9 REMARK 620 4 0RV A 301 NAN 103.9 149.9 81.2 REMARK 620 5 0RV A 301 OAI 96.0 104.5 140.0 58.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 103.4 REMARK 620 3 HIS B 189 NE2 109.3 109.2 REMARK 620 4 0RV B 301 OAF 128.3 98.0 107.0 REMARK 620 N 1 2 3 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 107.3 REMARK 620 3 HIS B 250 NE2 87.7 113.9 REMARK 620 4 0RV B 301 NAN 102.2 147.5 80.3 REMARK 620 5 0RV B 301 OAF 92.1 110.5 133.4 54.2 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 0RV 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 0RV B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3Q6X RELATED DB: PDB REMARK 900 RELATED ID: 3SPU RELATED DB: PDB REMARK 900 RELATED ID: 4EXY RELATED DB: PDB REMARK 900 RELATED ID: 4EY2 RELATED DB: PDB REMARK 900 RELATED ID: 4EYB RELATED DB: PDB REMARK 900 RELATED ID: 4EYF RELATED DB: PDB REMARK 900 RELATED ID: 4EYL RELATED DB: PDB DBREF 4EYL A 1 270 UNP C7C422 BLAN1_KLEPN 1 270 DBREF 4EYL B 1 270 UNP C7C422 BLAN1_KLEPN 1 270 SEQADV 4EYL LEU A 271 UNP C7C422 EXPRESSION TAG SEQADV 4EYL VAL A 272 UNP C7C422 EXPRESSION TAG SEQADV 4EYL LEU B 271 UNP C7C422 EXPRESSION TAG SEQADV 4EYL VAL B 272 UNP C7C422 EXPRESSION TAG SEQRES 1 A 272 MET GLU LEU PRO ASN ILE MET HIS PRO VAL ALA LYS LEU SEQRES 2 A 272 SER THR ALA LEU ALA ALA ALA LEU MET LEU SER GLY CYS SEQRES 3 A 272 MET PRO GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET SEQRES 4 A 272 GLU THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG SEQRES 5 A 272 GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU SEQRES 6 A 272 ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU SEQRES 7 A 272 ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR SEQRES 8 A 272 ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP SEQRES 9 A 272 ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL SEQRES 10 A 272 VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP SEQRES 11 A 272 ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA SEQRES 12 A 272 LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA SEQRES 13 A 272 ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL SEQRES 14 A 272 GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL SEQRES 15 A 272 PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR SEQRES 16 A 272 VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS SEQRES 17 A 272 LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU SEQRES 18 A 272 GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG SEQRES 19 A 272 ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL SEQRES 20 A 272 MET SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR SEQRES 21 A 272 HIS THR ALA ARG MET ALA ASP LYS LEU ARG LEU VAL SEQRES 1 B 272 MET GLU LEU PRO ASN ILE MET HIS PRO VAL ALA LYS LEU SEQRES 2 B 272 SER THR ALA LEU ALA ALA ALA LEU MET LEU SER GLY CYS SEQRES 3 B 272 MET PRO GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET SEQRES 4 B 272 GLU THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG SEQRES 5 B 272 GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU SEQRES 6 B 272 ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU SEQRES 7 B 272 ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR SEQRES 8 B 272 ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP SEQRES 9 B 272 ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL SEQRES 10 B 272 VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP SEQRES 11 B 272 ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA SEQRES 12 B 272 LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA SEQRES 13 B 272 ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL SEQRES 14 B 272 GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL SEQRES 15 B 272 PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR SEQRES 16 B 272 VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS SEQRES 17 B 272 LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU SEQRES 18 B 272 GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG SEQRES 19 B 272 ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL SEQRES 20 B 272 MET SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR SEQRES 21 B 272 HIS THR ALA ARG MET ALA ASP LYS LEU ARG LEU VAL HET 0RV A 301 49 HET ZN A 302 1 HET ZN A 303 1 HET 0RV B 301 49 HET ZN B 302 1 HET ZN B 303 1 HETNAM 0RV (2S)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-4-{[(3S,5S)- HETNAM 2 0RV 5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-3- HETNAM 3 0RV METHYL-2H-PYRRO LE-5-CARBOXYLIC ACID HETNAM ZN ZINC ION HETSYN 0RV MEROPENEM, HYDROXYLATED FORM FORMUL 3 0RV 2(C17 H25 N3 O6 S) FORMUL 4 ZN 4(ZN 2+) FORMUL 9 HOH *161(H2 O) HELIX 1 1 THR A 94 ILE A 109 1 16 HELIX 2 2 HIS A 122 GLY A 127 1 6 HELIX 3 3 GLY A 128 ALA A 135 1 8 HELIX 4 4 ALA A 143 GLY A 153 1 11 HELIX 5 5 GLU A 170 ALA A 174 5 5 HELIX 6 6 HIS A 228 PHE A 240 1 13 HELIX 7 7 ARG A 256 VAL A 272 1 17 HELIX 8 8 THR B 94 ILE B 109 1 16 HELIX 9 9 HIS B 122 GLY B 127 1 6 HELIX 10 10 GLY B 128 ALA B 135 1 8 HELIX 11 11 ALA B 143 ALA B 149 1 7 HELIX 12 12 PRO B 150 GLY B 153 5 4 HELIX 13 13 GLU B 170 ALA B 174 5 5 HELIX 14 14 HIS B 228 PHE B 240 1 13 HELIX 15 15 ARG B 256 LEU B 271 1 16 SHEET 1 A 8 ASP A 43 PHE A 46 0 SHEET 2 A 8 LEU A 49 ALA A 55 -1 O LEU A 49 N PHE A 46 SHEET 3 A 8 VAL A 58 LEU A 65 -1 O VAL A 58 N LEU A 54 SHEET 4 A 8 VAL A 73 ASP A 82 -1 O ILE A 79 N TRP A 59 SHEET 5 A 8 ARG A 85 VAL A 89 -1 O LEU A 87 N VAL A 80 SHEET 6 A 8 VAL A 113 VAL A 117 1 O VAL A 117 N VAL A 88 SHEET 7 A 8 ALA A 138 ASN A 142 1 O ALA A 138 N ALA A 116 SHEET 8 A 8 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141 SHEET 1 B 4 LEU A 180 PHE A 183 0 SHEET 2 B 4 THR A 195 ILE A 198 -1 O GLY A 197 N LYS A 181 SHEET 3 B 4 ILE A 203 PHE A 205 -1 O PHE A 205 N VAL A 196 SHEET 4 B 4 MET A 245 VAL A 247 1 O VAL A 247 N ALA A 204 SHEET 1 C 9 GLN B 37 GLN B 38 0 SHEET 2 C 9 GLN B 44 PHE B 46 -1 O ARG B 45 N GLN B 37 SHEET 3 C 9 LEU B 49 ALA B 55 -1 O PHE B 51 N GLN B 44 SHEET 4 C 9 VAL B 58 TYR B 64 -1 O VAL B 58 N LEU B 54 SHEET 5 C 9 ALA B 74 ASP B 82 -1 O ILE B 79 N TRP B 59 SHEET 6 C 9 ARG B 85 VAL B 89 -1 O LEU B 87 N VAL B 80 SHEET 7 C 9 VAL B 113 VAL B 118 1 O VAL B 117 N VAL B 88 SHEET 8 C 9 ALA B 138 ASN B 142 1 O TYR B 140 N VAL B 118 SHEET 9 C 9 HIS B 159 LEU B 161 1 O LEU B 161 N ALA B 141 SHEET 1 D 4 LEU B 180 PHE B 183 0 SHEET 2 D 4 THR B 195 ILE B 198 -1 O GLY B 197 N LYS B 181 SHEET 3 D 4 ILE B 203 PHE B 205 -1 O PHE B 205 N VAL B 196 SHEET 4 D 4 MET B 245 VAL B 247 1 O MET B 245 N ALA B 204 LINK NE2 HIS A 120 ZN ZN A 303 1555 1555 2.15 LINK ND1 HIS A 122 ZN ZN A 303 1555 1555 2.11 LINK OD2 ASP A 124 ZN ZN A 302 1555 1555 2.29 LINK NE2 HIS A 189 ZN ZN A 303 1555 1555 2.08 LINK SG CYS A 208 ZN ZN A 302 1555 1555 2.34 LINK NE2 HIS A 250 ZN ZN A 302 1555 1555 2.08 LINK NAN 0RV A 301 ZN ZN A 302 1555 1555 2.21 LINK OAI 0RV A 301 ZN ZN A 302 1555 1555 2.46 LINK OAI 0RV A 301 ZN ZN A 303 1555 1555 2.28 LINK NE2 HIS B 120 ZN ZN B 303 1555 1555 2.11 LINK ND1 HIS B 122 ZN ZN B 303 1555 1555 2.05 LINK OD2 ASP B 124 ZN ZN B 302 1555 1555 2.15 LINK NE2 HIS B 189 ZN ZN B 303 1555 1555 2.14 LINK SG CYS B 208 ZN ZN B 302 1555 1555 2.34 LINK NE2 HIS B 250 ZN ZN B 302 1555 1555 2.02 LINK NAN 0RV B 301 ZN ZN B 302 1555 1555 2.32 LINK OAF 0RV B 301 ZN ZN B 302 1555 1555 2.68 LINK OAF 0RV B 301 ZN ZN B 303 1555 1555 2.24 SITE 1 AC1 11 HIS A 122 GLN A 123 ASP A 124 HIS A 189 SITE 2 AC1 11 CYS A 208 LYS A 211 GLY A 219 ASN A 220 SITE 3 AC1 11 HIS A 250 ZN A 302 ZN A 303 SITE 1 AC2 4 ASP A 124 CYS A 208 HIS A 250 0RV A 301 SITE 1 AC3 4 HIS A 120 HIS A 122 HIS A 189 0RV A 301 SITE 1 AC4 13 HIS B 122 GLN B 123 ASP B 124 HIS B 189 SITE 2 AC4 13 CYS B 208 LYS B 211 SER B 217 ASN B 220 SITE 3 AC4 13 HIS B 250 LEU B 271 ZN B 302 ZN B 303 SITE 4 AC4 13 HOH B 408 SITE 1 AC5 4 ASP B 124 CYS B 208 HIS B 250 0RV B 301 SITE 1 AC6 4 HIS B 120 HIS B 122 HIS B 189 0RV B 301 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