HEADER HYDROLASE 18-MAR-18 5ZJ2 TITLE CRYSTAL STRUCTURE OF NDM-1 IN COMPLEX WITH D-CAPTOPRIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE TYPE 2; COMPND 3 CHAIN: A; 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(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRHISMBP KEYWDS NDM-1, METALLO-BETA-LACTAMASE, ANTIBIOTIC RESISTENT, INHIBITOR, THIO KEYWDS 2 COMPOUNDS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,Q.HAO REVDAT 3 22-NOV-23 5ZJ2 1 REMARK REVDAT 2 16-DEC-20 5ZJ2 1 JRNL REVDAT 1 20-MAR-19 5ZJ2 0 JRNL AUTH G.MA,S.WANG,K.WU,W.ZHANG,A.AHMAD,Q.HAO,X.LEI,H.ZHANG JRNL TITL STRUCTURE-GUIDED OPTIMIZATION OF D-CAPTOPRIL FOR DISCOVERY JRNL TITL 2 OF POTENT NDM-1 INHIBITORS JRNL REF BIOORG.MED.CHEM. V. 29 2020 JRNL REFN ESSN 1464-3391 JRNL DOI 10.1016/J.BMC.2020.115902 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 73459 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) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3859 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) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2846 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 155 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1701 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 294 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : 0.47000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.48000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.030 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.031 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.098 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1807 ; 0.008 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 1607 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2471 ; 1.516 ; 1.744 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3761 ; 0.635 ; 1.722 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 243 ; 6.846 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;29.125 ;20.312 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 246 ;12.974 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;19.676 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 243 ; 0.355 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2106 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 338 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 3414 ; 3.302 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 185 ;28.713 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3477 ;10.601 ; 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 : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 42 A 46 REMARK 3 ORIGIN FOR THE GROUP (A): 34.8039 33.9560 47.6209 REMARK 3 T TENSOR REMARK 3 T11: 0.4515 T22: 0.1835 REMARK 3 T33: 0.0584 T12: 0.0106 REMARK 3 T13: 0.0012 T23: 0.0248 REMARK 3 L TENSOR REMARK 3 L11: 7.0937 L22: 5.0821 REMARK 3 L33: 11.7400 L12: -5.1211 REMARK 3 L13: -8.5601 L23: 6.5297 REMARK 3 S TENSOR REMARK 3 S11: -0.4677 S12: 0.3816 S13: -0.4670 REMARK 3 S21: 1.0293 S22: -0.1613 S23: 0.3503 REMARK 3 S31: 0.4764 S32: -0.6020 S33: 0.6291 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 47 A 70 REMARK 3 ORIGIN FOR THE GROUP (A): 32.6730 34.1182 39.0774 REMARK 3 T TENSOR REMARK 3 T11: 0.0697 T22: 0.1187 REMARK 3 T33: 0.0609 T12: -0.0224 REMARK 3 T13: 0.0328 T23: -0.0415 REMARK 3 L TENSOR REMARK 3 L11: 1.4395 L22: 4.9999 REMARK 3 L33: 1.3049 L12: 0.7769 REMARK 3 L13: -0.5283 L23: 0.2724 REMARK 3 S TENSOR REMARK 3 S11: 0.0629 S12: -0.1459 S13: 0.1540 REMARK 3 S21: -0.0095 S22: -0.0790 S23: 0.2078 REMARK 3 S31: -0.1310 S32: -0.0067 S33: 0.0161 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 71 A 210 REMARK 3 ORIGIN FOR THE GROUP (A): 35.7350 25.4835 28.2323 REMARK 3 T TENSOR REMARK 3 T11: 0.0397 T22: 0.0672 REMARK 3 T33: 0.0411 T12: 0.0112 REMARK 3 T13: 0.0163 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.5003 L22: 1.8266 REMARK 3 L33: 1.4034 L12: 0.2637 REMARK 3 L13: -0.2756 L23: 0.0600 REMARK 3 S TENSOR REMARK 3 S11: 0.0070 S12: -0.0710 S13: -0.0178 REMARK 3 S21: -0.1563 S22: -0.1148 S23: 0.0398 REMARK 3 S31: 0.0531 S32: -0.0079 S33: 0.1078 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 211 A 220 REMARK 3 ORIGIN FOR THE GROUP (A): 19.3646 40.2584 28.7574 REMARK 3 T TENSOR REMARK 3 T11: 0.5766 T22: 0.3679 REMARK 3 T33: 0.4510 T12: -0.1581 REMARK 3 T13: -0.0569 T23: -0.3366 REMARK 3 L TENSOR REMARK 3 L11: 2.7754 L22: 12.0908 REMARK 3 L33: 5.4900 L12: 3.1929 REMARK 3 L13: 2.3309 L23: -2.7188 REMARK 3 S TENSOR REMARK 3 S11: -0.8818 S12: -0.2760 S13: 0.8221 REMARK 3 S21: -0.5823 S22: 0.0880 S23: 0.6117 REMARK 3 S31: -1.1532 S32: -0.3532 S33: 0.7938 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 221 A 265 REMARK 3 ORIGIN FOR THE GROUP (A): 19.1263 30.5510 26.0150 REMARK 3 T TENSOR REMARK 3 T11: 0.0245 T22: 0.1245 REMARK 3 T33: 0.2593 T12: 0.0052 REMARK 3 T13: -0.0663 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 3.2500 L22: 1.2250 REMARK 3 L33: 1.1215 L12: -0.6225 REMARK 3 L13: -0.1934 L23: -0.1583 REMARK 3 S TENSOR REMARK 3 S11: 0.0822 S12: 0.1674 S13: 0.2550 REMARK 3 S21: -0.1698 S22: 0.0342 S23: 0.4545 REMARK 3 S31: 0.0070 S32: -0.2447 S33: -0.1164 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 266 A 270 REMARK 3 ORIGIN FOR THE GROUP (A): 13.5337 37.8450 17.1572 REMARK 3 T TENSOR REMARK 3 T11: 0.3402 T22: 0.2362 REMARK 3 T33: 0.1832 T12: 0.1190 REMARK 3 T13: -0.0397 T23: 0.1600 REMARK 3 L TENSOR REMARK 3 L11: 12.2044 L22: 10.7042 REMARK 3 L33: 13.9088 L12: 6.6194 REMARK 3 L13: -6.2371 L23: -3.4949 REMARK 3 S TENSOR REMARK 3 S11: 0.0925 S12: 1.2293 S13: 0.9966 REMARK 3 S21: -0.8363 S22: 0.4669 S23: 0.4244 REMARK 3 S31: 0.0779 S32: -0.6374 S33: -0.5594 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5ZJ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300007166. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-16 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 : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82705 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.67100 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: 3Q6X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH5.5, 15% PEG3350, 20MM REMARK 280 L-PROLINE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.94600 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 THR A 41 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 OD1 ASP A 66 O HOH A 578 2757 2.05 REMARK 500 OD2 ASP A 66 O HOH A 574 2757 2.14 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 90 142.48 76.30 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 52 0.10 SIDE CHAIN REMARK 500 ARG A 85 0.08 SIDE CHAIN 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 694 DISTANCE = 6.21 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 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 99.0 REMARK 620 3 HIS A 189 NE2 101.3 114.9 REMARK 620 4 MCO A 303 S 136.1 109.0 96.7 REMARK 620 N 1 2 3 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 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 111.0 REMARK 620 3 HIS A 250 NE2 91.4 104.6 REMARK 620 4 MCO A 303 S 117.5 112.0 118.3 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 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 MCO A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ZIO RELATED DB: PDB REMARK 900 NDM-1 IN COMPLEX WITH L-CAPTOPRIL REMARK 900 RELATED ID: 5ZJ1 RELATED DB: PDB REMARK 900 NDM-1 IN COMPLEX WITH D-CAPTOPRIL DERIVATIVE CYT-14 DBREF 5ZJ2 A 29 270 UNP C7C422 BLAN1_KLEPN 29 270 SEQRES 1 A 242 GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU THR SEQRES 2 A 242 GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU SEQRES 3 A 242 ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET SEQRES 4 A 242 PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL SEQRES 5 A 242 ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP SEQRES 6 A 242 THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS SEQRES 7 A 242 GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR SEQRES 8 A 242 HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU SEQRES 9 A 242 HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER SEQRES 10 A 242 ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN SEQRES 11 A 242 HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO SEQRES 12 A 242 ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR SEQRES 13 A 242 PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY SEQRES 14 A 242 ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE SEQRES 15 A 242 LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP SEQRES 16 A 242 ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE SEQRES 17 A 242 GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER SEQRES 18 A 242 HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR SEQRES 19 A 242 ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 301 1 HET ZN A 302 1 HET MCO A 303 14 HETNAM ZN ZINC ION HETNAM MCO 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2- HETNAM 2 MCO CARBOXYLIC ACID FORMUL 2 ZN 2(ZN 2+) FORMUL 4 MCO C9 H15 N O3 S FORMUL 5 HOH *294(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 CYS A 208 ILE A 210 5 3 HELIX 7 AA7 HIS A 228 PHE A 240 1 13 HELIX 8 AA8 ARG A 256 LYS A 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 LEU A 49 N PHE A 46 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 VAL A 73 N LEU A 65 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 GLY A 197 N LYS A 181 SHEET 3 AA2 4 ILE A 203 GLY A 207 -1 O PHE A 205 N VAL A 196 SHEET 4 AA2 4 MET A 245 MET A 248 1 O VAL A 247 N GLY A 206 LINK NE2 HIS A 120 ZN ZN A 302 1555 1555 2.05 LINK ND1 HIS A 122 ZN ZN A 302 1555 1555 2.07 LINK OD2 ASP A 124 ZN ZN A 301 1555 1555 1.92 LINK NE2 HIS A 189 ZN ZN A 302 1555 1555 2.04 LINK SG CYS A 208 ZN ZN A 301 1555 1555 2.29 LINK NE2 HIS A 250 ZN ZN A 301 1555 1555 2.06 LINK ZN ZN A 301 S MCO A 303 1555 1555 2.32 LINK ZN ZN A 302 S MCO A 303 1555 1555 2.32 SITE 1 AC1 5 ASP A 124 CYS A 208 HIS A 250 ZN A 302 SITE 2 AC1 5 MCO A 303 SITE 1 AC2 5 HIS A 120 HIS A 122 HIS A 189 ZN A 301 SITE 2 AC2 5 MCO A 303 SITE 1 AC3 15 PHE A 70 VAL A 73 TRP A 93 HIS A 122 SITE 2 AC3 15 ASP A 124 HIS A 189 GLY A 219 ASN A 220 SITE 3 AC3 15 HIS A 250 ZN A 301 ZN A 302 HOH A 405 SITE 4 AC3 15 HOH A 409 HOH A 412 HOH A 487 CRYST1 41.698 59.892 42.138 90.00 97.78 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.023982 0.000000 0.003277 0.00000 SCALE2 0.000000 0.016697 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023952 0.00000