HEADER HYDROLASE 15-JUN-11 3ZR9 TITLE STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE 1 (NDM-1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE NDM-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BETA-LACTAMASE, RESIDUES 42-270; COMPND 5 SYNONYM: NDM1, NDM-1, METALLO-BETA-LACTAMASE NDM-1; COMPND 6 EC: 3.5.2.6; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: POPINF KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.L.GREEN,A.VERMA,R.J.OWENS,S.E.V.PHILLIPS,S.B.CARR REVDAT 5 20-DEC-23 3ZR9 1 REMARK LINK REVDAT 4 30-NOV-11 3ZR9 1 JRNL REVDAT 3 03-AUG-11 3ZR9 1 REMARK VERSN REVDAT 2 06-JUL-11 3ZR9 1 REMARK DBREF SEQADV HELIX REVDAT 2 2 1 SHEET LINK SITE ATOM REVDAT 2 3 1 ANISOU TER REVDAT 1 29-JUN-11 3ZR9 0 JRNL AUTH V.L.GREEN,A.VERMA,R.J.OWENS,S.E.PHILLIPS,S.B.CARR JRNL TITL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE 1 (NDM-1). JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 67 1160 2011 JRNL REFN ESSN 1744-3091 JRNL PMID 22102018 JRNL DOI 10.1107/S1744309111029654 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 23970 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1288 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) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1733 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1696 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 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): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.880 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1748 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2386 ; 1.577 ; 1.927 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 234 ; 8.300 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;32.610 ;24.595 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 249 ;14.495 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;16.528 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 266 ; 0.141 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1364 ; 0.013 ; 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): 1150 ; 1.556 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1823 ; 2.221 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 598 ; 3.249 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 562 ; 4.538 ; 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 : 3 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 40 A 63 REMARK 3 ORIGIN FOR THE GROUP (A): 39.5711 16.7511 13.3957 REMARK 3 T TENSOR REMARK 3 T11: 0.1241 T22: 0.2643 REMARK 3 T33: 0.1392 T12: -0.0995 REMARK 3 T13: -0.0475 T23: -0.0389 REMARK 3 L TENSOR REMARK 3 L11: 1.1275 L22: 2.4553 REMARK 3 L33: 0.9386 L12: 0.6831 REMARK 3 L13: -0.5363 L23: 0.3058 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: 0.0909 S13: -0.0416 REMARK 3 S21: 0.1420 S22: 0.0287 S23: -0.2875 REMARK 3 S31: -0.2122 S32: 0.3336 S33: -0.0149 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 64 A 72 REMARK 3 ORIGIN FOR THE GROUP (A): 25.1776 29.6042 17.1745 REMARK 3 T TENSOR REMARK 3 T11: 0.4874 T22: 0.1802 REMARK 3 T33: 0.2703 T12: 0.1213 REMARK 3 T13: -0.0234 T23: -0.1601 REMARK 3 L TENSOR REMARK 3 L11: 27.7646 L22: 29.8706 REMARK 3 L33: 19.4118 L12: -3.2969 REMARK 3 L13: 17.9691 L23: -0.5011 REMARK 3 S TENSOR REMARK 3 S11: -1.1693 S12: -1.2548 S13: 1.2900 REMARK 3 S21: 1.4474 S22: -0.3289 S23: 1.6361 REMARK 3 S31: -2.2222 S32: -1.9136 S33: 1.4982 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 73 A 268 REMARK 3 ORIGIN FOR THE GROUP (A): 26.6300 10.8850 14.0360 REMARK 3 T TENSOR REMARK 3 T11: 0.0542 T22: 0.0858 REMARK 3 T33: 0.0828 T12: -0.0176 REMARK 3 T13: 0.0077 T23: -0.0804 REMARK 3 L TENSOR REMARK 3 L11: 0.8666 L22: 1.3515 REMARK 3 L33: 2.3546 L12: 0.2498 REMARK 3 L13: 0.4867 L23: -0.5013 REMARK 3 S TENSOR REMARK 3 S11: 0.0988 S12: 0.1044 S13: -0.0534 REMARK 3 S21: 0.1196 S22: -0.0622 S23: -0.0093 REMARK 3 S31: -0.1773 S32: 0.1329 S33: -0.0366 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 3ZR9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1290048707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9163 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25258 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 28.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 12.20 REMARK 200 R MERGE FOR SHELL (I) : 0.76000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 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: PDB ENTRY 2WHG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5 MM COCL2, 5 MM NICL2, 5 MM MGCL2, 5 REMARK 280 MM CDCL2, 100 MM HEPES PH 7.5, 12% (W/V) PEG 3350. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 60.15000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 60.15000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 44.05000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 60.15000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 60.15000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 44.05000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 60.15000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 60.15000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 44.05000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 60.15000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 60.15000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 44.05000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 60.15000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 60.15000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 44.05000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 60.15000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 60.15000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 44.05000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 60.15000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 60.15000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 44.05000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 60.15000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 60.15000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 44.05000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 70910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -680.3 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NI NI A 277 LIES ON A SPECIAL POSITION. 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 PRO A 41 CG CD REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 LYS A 242 CG CD CE NZ REMARK 470 ARG A 264 CG CD NE CZ NH1 NH2 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 NI NI A 275 O HOH A 2102 1.70 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 PRO A 41 C - N - CA ANGL. DEV. = 17.1 DEGREES REMARK 500 ASP A 124 CB - CG - OD1 ANGL. DEV. = 6.7 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 90 144.00 74.85 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 GLY A 40 PRO A 41 141.64 REMARK 500 ASP A 82 GLY A 83 -126.25 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 CO A 274 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 95 OD2 REMARK 620 2 ASP A 130 OD2 104.7 REMARK 620 3 HOH A2029 O 101.7 85.6 REMARK 620 4 HOH A2030 O 76.7 81.3 165.9 REMARK 620 5 HOH A2031 O 86.9 168.1 94.7 99.2 REMARK 620 6 HOH A2051 O 157.8 92.4 93.4 92.4 75.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 273 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 95.5 REMARK 620 3 HIS A 189 NE2 104.2 105.5 REMARK 620 4 HOH A2043 O 114.7 106.3 126.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 276 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 90.8 REMARK 620 3 HIS A 250 NE2 80.8 103.2 REMARK 620 4 HOH A2043 O 77.7 97.5 150.3 REMARK 620 5 HOH A2048 O 77.6 166.5 82.0 73.4 REMARK 620 6 HOH A2090 O 163.6 104.9 90.8 104.3 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 279 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 152 OE2 REMARK 620 2 GLU A 152 OE1 52.9 REMARK 620 3 GLU A 170 OE2 84.5 119.6 REMARK 620 4 GLU A 170 OE1 103.3 90.7 56.2 REMARK 620 5 ASP A 223 OD2 96.4 86.9 145.1 153.1 REMARK 620 6 ASP A 223 OD1 99.7 132.1 90.7 136.7 54.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 277 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 159 NE2 REMARK 620 2 HIS A 159 NE2 176.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 278 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 261 ND1 REMARK 620 2 HOH A2113 O 63.4 REMARK 620 3 HOH A2115 O 104.4 76.1 REMARK 620 4 HOH A2116 O 96.6 113.5 159.0 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 273 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 274 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 275 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 278 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 279 DBREF 3ZR9 A 42 270 UNP C7C422 BLAN1_KLEPN 42 270 SEQADV 3ZR9 GLY A 40 UNP C7C422 EXPRESSION TAG SEQADV 3ZR9 PRO A 41 UNP C7C422 EXPRESSION TAG SEQRES 1 A 231 GLY PRO GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG SEQRES 2 A 231 GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU SEQRES 3 A 231 ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU SEQRES 4 A 231 ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR SEQRES 5 A 231 ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP SEQRES 6 A 231 ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL SEQRES 7 A 231 VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP SEQRES 8 A 231 ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA SEQRES 9 A 231 LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA SEQRES 10 A 231 ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL SEQRES 11 A 231 GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL SEQRES 12 A 231 PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR SEQRES 13 A 231 VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS SEQRES 14 A 231 LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU SEQRES 15 A 231 GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG SEQRES 16 A 231 ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL SEQRES 17 A 231 MET SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR SEQRES 18 A 231 HIS THR ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 273 1 HET CO A 274 1 HET NI A 275 1 HET CD A 276 1 HET NI A 277 1 HET NI A 278 1 HET NI A 279 1 HETNAM ZN ZINC ION HETNAM CO COBALT (II) ION HETNAM NI NICKEL (II) ION HETNAM CD CADMIUM ION FORMUL 2 ZN ZN 2+ FORMUL 3 CO CO 2+ FORMUL 4 NI 4(NI 2+) FORMUL 5 CD CD 2+ FORMUL 9 HOH *116(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 ALA A 149 1 7 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 LYS A 268 1 13 SHEET 1 AA 8 GLN A 44 PHE A 46 0 SHEET 2 AA 8 LEU A 49 ALA A 55 -1 O LEU A 49 N PHE A 46 SHEET 3 AA 8 VAL A 58 MET A 67 -1 O VAL A 58 N LEU A 54 SHEET 4 AA 8 PHE A 70 ASP A 82 -1 O PHE A 70 N MET A 67 SHEET 5 AA 8 ARG A 85 VAL A 89 -1 O ARG A 85 N ASP A 82 SHEET 6 AA 8 VAL A 113 VAL A 117 1 N ALA A 114 O VAL A 86 SHEET 7 AA 8 ALA A 138 ASN A 142 1 O ALA A 138 N ALA A 116 SHEET 8 AA 8 HIS A 159 LEU A 161 1 O HIS A 159 N ALA A 141 SHEET 1 AB 4 LEU A 180 PHE A 183 0 SHEET 2 AB 4 THR A 195 ILE A 198 -1 O THR A 195 N PHE A 183 SHEET 3 AB 4 ILE A 203 GLY A 207 -1 O ILE A 203 N ILE A 198 SHEET 4 AB 4 MET A 245 MET A 248 1 O MET A 245 N ALA A 204 LINK OD2 ASP A 95 CO CO A 274 1555 1555 2.38 LINK NE2 HIS A 120 ZN ZN A 273 1555 1555 2.15 LINK ND1 HIS A 122 ZN ZN A 273 1555 1555 1.98 LINK OD2 ASP A 124 CD CD A 276 1555 1555 2.43 LINK OD2 ASP A 130 CO CO A 274 1555 1555 2.11 LINK OE2 GLU A 152 NI NI A 279 4555 1555 2.40 LINK OE1 GLU A 152 NI NI A 279 4555 1555 2.61 LINK NE2 HIS A 159 NI NI A 277 1555 1555 2.19 LINK NE2 HIS A 159 NI NI A 277 6555 1555 2.19 LINK OE2 GLU A 170 NI NI A 279 1555 1555 2.32 LINK OE1 GLU A 170 NI NI A 279 1555 1555 2.29 LINK NE2 HIS A 189 ZN ZN A 273 1555 1555 2.16 LINK SG CYS A 208 CD CD A 276 1555 1555 2.58 LINK OD2 ASP A 223 NI NI A 279 4555 1555 2.40 LINK OD1 ASP A 223 NI NI A 279 4555 1555 2.17 LINK NE2 HIS A 228 NI NI A 275 1555 1555 2.44 LINK NE2 HIS A 250 CD CD A 276 1555 1555 2.33 LINK ND1 HIS A 261 NI NI A 278 1555 1555 2.60 LINK ZN ZN A 273 O HOH A2043 1555 1555 1.93 LINK CO CO A 274 O HOH A2029 1555 1555 2.24 LINK CO CO A 274 O HOH A2030 1555 1555 1.87 LINK CO CO A 274 O HOH A2031 1555 1555 2.38 LINK CO CO A 274 O HOH A2051 1555 1555 2.46 LINK CD CD A 276 O HOH A2043 1555 1555 2.38 LINK CD CD A 276 O HOH A2048 1555 1555 2.71 LINK CD CD A 276 O HOH A2090 1555 1555 2.54 LINK NI NI A 278 O HOH A2113 1555 1555 2.28 LINK NI NI A 278 O HOH A2115 1555 1555 2.54 LINK NI NI A 278 O HOH A2116 1555 1555 2.64 SITE 1 AC1 5 HIS A 120 HIS A 122 HIS A 189 CD A 276 SITE 2 AC1 5 HOH A2043 SITE 1 AC2 6 ASP A 95 ASP A 130 HOH A2029 HOH A2030 SITE 2 AC2 6 HOH A2031 HOH A2051 SITE 1 AC3 2 HIS A 228 HOH A2102 SITE 1 AC4 7 ASP A 124 CYS A 208 HIS A 250 ZN A 273 SITE 2 AC4 7 HOH A2043 HOH A2048 HOH A2090 SITE 1 AC5 1 HIS A 159 SITE 1 AC6 4 HIS A 261 HOH A2113 HOH A2115 HOH A2116 SITE 1 AC7 3 GLU A 152 GLU A 170 ASP A 223 CRYST1 120.300 120.300 88.100 90.00 90.00 90.00 I 4 2 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 0.008313 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008313 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011351 0.00000