PDB Short entry for 3LVZ HEADER HYDROLASE 23-FEB-10 3LVZ TITLE NEW REFINEMENT OF THE CRYSTAL STRUCTURE OF BJP-1, A SUBCLASS B3 TITLE 2 METALLO-BETA-LACTAMASE OF BRADYRHIZOBIUM JAPONICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BLR6230 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SUBCLASS B3 METALLO-BETA-LACTAMASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM JAPONICUM; SOURCE 3 ORGANISM_TAXID: 224911; SOURCE 4 STRAIN: USDA 100; SOURCE 5 GENE: BLR6230, BRADYRHIZOBIUM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-9A KEYWDS CLASS B3 METALLO-BETA-LACTAMASE, HYDROLASE, BETA-LACTAM HYDROLYSIS EXPDTA X-RAY DIFFRACTION AUTHOR J.D.DOCQUIER,M.BENVENUTI,V.CALDERONE,M.STOCZKO,G.M.ROSSOLINI, AUTHOR 2 S.MANGANI REVDAT 1 12-JAN-11 3LVZ 0 JRNL AUTH J.D.DOCQUIER,M.BENVENUTI,V.CALDERONE,M.STOCZKO,N.MENCIASSI, JRNL AUTH 2 G.M.ROSSOLINI,S.MANGANI JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE SUBCLASS B3 JRNL TITL 2 METALLO-BETA-LACTAMASE BJP-1: RATIONAL BASIS FOR SUBSTRATE JRNL TITL 3 SPECIFICITY AND INTERACTION WITH SULFONAMIDES. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 54 4343 2010 JRNL REFN ISSN 0066-4804 JRNL PMID 20696874 JRNL DOI 10.1128/AAC.00409-10 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 79602 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT : 8006 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4237 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE SET COUNT : 434 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4109 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 482 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.09 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) : 0.00000 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): 0.065 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.036 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.000 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4266 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2844 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5804 ; 2.204 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7004 ; 1.093 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 563 ; 5.900 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;33.152 ;24.824 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 717 ;12.124 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.990 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 661 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4789 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 816 ; 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): 2735 ; 1.273 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1118 ; 0.446 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4393 ; 2.046 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1531 ; 2.993 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1401 ; 4.627 ; 4.500 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 : 2 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 23 A 294 REMARK 3 ORIGIN FOR THE GROUP (A): -0.3559 1.4363 0.4558 REMARK 3 T TENSOR REMARK 3 T11: 0.0037 T22: 0.0126 REMARK 3 T33: 0.0030 T12: 0.0012 REMARK 3 T13: -0.0008 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.6926 L22: 0.7588 REMARK 3 L33: 0.6242 L12: -0.3266 REMARK 3 L13: -0.1824 L23: 0.2826 REMARK 3 S TENSOR REMARK 3 S11: -0.0120 S12: -0.0825 S13: 0.0039 REMARK 3 S21: -0.0134 S22: 0.0357 S23: -0.0059 REMARK 3 S31: -0.0278 S32: 0.0523 S33: -0.0237 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 : B 22 B 294 REMARK 3 ORIGIN FOR THE GROUP (A): 9.6977 -14.6764 -36.6101 REMARK 3 T TENSOR REMARK 3 T11: 0.0045 T22: 0.0103 REMARK 3 T33: 0.0094 T12: -0.0029 REMARK 3 T13: -0.0030 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.9241 L22: 0.5225 REMARK 3 L33: 0.6076 L12: 0.1871 REMARK 3 L13: -0.1277 L23: -0.1332 REMARK 3 S TENSOR REMARK 3 S11: -0.0070 S12: 0.0815 S13: -0.0061 REMARK 3 S21: 0.0057 S22: 0.0379 S23: 0.0214 REMARK 3 S31: -0.0077 S32: -0.0278 S33: -0.0310 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 3LVZ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-10. REMARK 100 THE RCSB ID CODE IS RCSB057798. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2813 REMARK 200 MONOCHROMATOR : SI(111) LIQUID NITROGEN COOLED REMARK 200 CHANNEL-CUT SILICON MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87611 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 38.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.33600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30-35% PEG 4000, 0.5M SODIUM ACETATE, REMARK 280 5MM ZNCL2 PH 8.0-8.5, 0.1M TRISHCL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 LEU A 4 REMARK 465 THR A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 7 REMARK 465 LEU A 8 REMARK 465 CYS A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 11 REMARK 465 THR A 12 REMARK 465 LEU A 13 REMARK 465 LEU A 14 REMARK 465 SER A 15 REMARK 465 THR A 16 REMARK 465 GLY A 17 REMARK 465 ALA A 18 REMARK 465 GLN A 19 REMARK 465 ALA A 20 REMARK 465 GLN A 21 REMARK 465 THR A 22 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 ARG B 3 REMARK 465 LEU B 4 REMARK 465 THR B 5 REMARK 465 ALA B 6 REMARK 465 ALA B 7 REMARK 465 LEU B 8 REMARK 465 CYS B 9 REMARK 465 ALA B 10 REMARK 465 LEU B 11 REMARK 465 THR B 12 REMARK 465 LEU B 13 REMARK 465 LEU B 14 REMARK 465 SER B 15 REMARK 465 THR B 16 REMARK 465 GLY B 17 REMARK 465 ALA B 18 REMARK 465 GLN B 19 REMARK 465 ALA B 20 REMARK 465 GLN B 21 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 LYS A 24 CG CD CE NZ REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 GLU A 143 CG CD OE1 OE2 REMARK 470 GLU A 254 CD OE1 OE2 REMARK 470 LYS A 256 CG CD CE NZ REMARK 470 ASP A 257 CG OD1 OD2 REMARK 470 LYS A 265 CD CE NZ REMARK 470 LYS A 282 CG CD CE NZ REMARK 470 LYS A 293 CG CD CE NZ REMARK 470 LYS A 294 CG CD CE NZ REMARK 470 MET B 31 CG SD CE REMARK 470 LYS B 32 CG CD CE NZ REMARK 470 LYS B 90 CD CE NZ REMARK 470 ARG B 126 CZ NH1 NH2 REMARK 470 GLU B 143 CG CD OE1 OE2 REMARK 470 GLU B 244 CG CD OE1 OE2 REMARK 470 GLU B 254 CD OE1 OE2 REMARK 470 ASP B 257 CG OD1 OD2 REMARK 470 LYS B 293 CG CD CE NZ REMARK 470 LYS B 294 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 39 CG GLU A 39 CD 0.098 REMARK 500 GLU A 112 CD GLU A 112 OE1 0.073 REMARK 500 CYS A 181 CB CYS A 181 SG -0.108 REMARK 500 GLU A 196 CD GLU A 196 OE2 -0.069 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 ASP A 166 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 CYS A 181 CA - CB - SG ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 224 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 MET A 255 CG - SD - CE ANGL. DEV. = -21.7 DEGREES REMARK 500 ASP B 53 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 MET B 79 CG - SD - CE ANGL. DEV. = -12.2 DEGREES REMARK 500 ASP B 144 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP B 236 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 252 NE - CZ - NH2 ANGL. DEV. = -3.2 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 LYS A 32 -99.40 -123.08 REMARK 500 ASP A 45 -122.86 53.85 REMARK 500 ASP A 70 174.20 68.74 REMARK 500 THR A 71 -158.15 -131.99 REMARK 500 ALA A 72 -155.71 -128.75 REMARK 500 ASP A 139 51.65 -152.38 REMARK 500 SER A 202 134.93 116.23 REMARK 500 ALA A 206 -123.99 52.14 REMARK 500 LYS B 32 -89.09 -111.84 REMARK 500 ASP B 45 -123.87 50.82 REMARK 500 ASP B 70 174.94 67.02 REMARK 500 ALA B 72 -154.21 -125.69 REMARK 500 ALA B 102 59.95 -97.73 REMARK 500 ASP B 139 48.04 -148.49 REMARK 500 SER B 202 135.31 114.54 REMARK 500 ALA B 206 -125.75 52.96 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 B 297 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 158 OE2 REMARK 620 2 LYS B 229 NZ 113.4 REMARK 620 3 HIS B 172 ND1 111.6 120.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 296 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 177 NE2 REMARK 620 2 HIS B 101 NE2 98.4 REMARK 620 3 HIS B 103 ND1 96.8 98.8 REMARK 620 4 HOH B 482 O 129.3 111.5 116.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 297 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 158 OE2 REMARK 620 2 LYS A 229 NZ 110.3 REMARK 620 3 HIS A 172 ND1 114.8 119.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 295 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 177 NE2 REMARK 620 2 HIS A 101 NE2 97.2 REMARK 620 3 HIS A 103 ND1 95.7 96.4 REMARK 620 4 HOH A 302 O 131.6 113.2 116.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 296 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 242 NE2 REMARK 620 2 ASP A 105 OD2 89.6 REMARK 620 3 HIS A 106 NE2 101.1 91.1 REMARK 620 4 HOH A 302 O 149.3 87.7 109.6 REMARK 620 5 HOH A 299 O 89.6 167.2 101.6 86.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 295 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 242 NE2 REMARK 620 2 HIS B 106 NE2 100.7 REMARK 620 3 ASP B 105 OD2 89.1 89.7 REMARK 620 4 HOH B 482 O 149.2 109.8 87.8 REMARK 620 5 HOH B 298 O 90.1 102.6 167.6 86.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 297 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GMN RELATED DB: PDB REMARK 900 SAME PROTEIN TO BE REPLACED BY THE PRESENT SUBMISSION REMARK 900 RELATED ID: 1K07 RELATED DB: PDB REMARK 900 SUBCLASS B3 BETA-LACTAMASE FEZ-1 FROM FLUORIBACTER GORMANII REMARK 900 RELATED ID: 2H6A RELATED DB: PDB REMARK 900 B3 SUBCLASS BETA-LACTAMASE L1 FROM STENOTROPHOMONAS REMARK 900 MALTOPHILIA DBREF 3LVZ A 1 294 UNP Q89GW5 Q89GW5_BRAJA 1 294 DBREF 3LVZ B 1 294 UNP Q89GW5 Q89GW5_BRAJA 1 294 SEQRES 1 A 294 MET ARG ARG LEU THR ALA ALA LEU CYS ALA LEU THR LEU SEQRES 2 A 294 LEU SER THR GLY ALA GLN ALA GLN THR ILE LYS ASP PHE SEQRES 3 A 294 LEU ALA VAL ALA MET LYS LYS TRP THR ALA PRO PHE GLU SEQRES 4 A 294 PRO PHE GLN LEU ILE ASP ASN ILE TYR TYR VAL GLY THR SEQRES 5 A 294 ASP GLY ILE ALA VAL TYR VAL ILE LYS THR SER GLN GLY SEQRES 6 A 294 LEU ILE LEU MET ASP THR ALA MET PRO GLN SER THR GLY SEQRES 7 A 294 MET ILE LYS ASP ASN ILE ALA LYS LEU GLY PHE LYS VAL SEQRES 8 A 294 ALA ASP ILE LYS LEU ILE LEU ASN THR HIS ALA HIS LEU SEQRES 9 A 294 ASP HIS THR GLY GLY PHE ALA GLU ILE LYS LYS GLU THR SEQRES 10 A 294 GLY ALA GLN LEU VAL ALA GLY GLU ARG ASP LYS PRO LEU SEQRES 11 A 294 LEU GLU GLY GLY TYR TYR PRO GLY ASP GLU LYS ASN GLU SEQRES 12 A 294 ASP LEU ALA PHE PRO ALA VAL LYS VAL ASP ARG ALA VAL SEQRES 13 A 294 LYS GLU GLY ASP ARG VAL THR LEU GLY ASP THR THR LEU SEQRES 14 A 294 THR ALA HIS ALA THR PRO GLY HIS SER PRO GLY CYS THR SEQRES 15 A 294 SER TRP GLU MET THR VAL LYS ASP GLY LYS GLU ASP ARG SEQRES 16 A 294 GLU VAL LEU PHE PHE CYS SER GLY THR VAL ALA LEU ASN SEQRES 17 A 294 ARG LEU VAL GLY GLN PRO THR TYR ALA GLY ILE VAL ASP SEQRES 18 A 294 ASP TYR ARG ALA THR PHE ALA LYS ALA LYS ALA MET LYS SEQRES 19 A 294 ILE ASP VAL LEU LEU GLY PRO HIS PRO GLU VAL TYR GLY SEQRES 20 A 294 MET GLN ALA LYS ARG ALA GLU MET LYS ASP GLY ALA PRO SEQRES 21 A 294 ASN PRO PHE ILE LYS PRO GLY GLU LEU VAL THR TYR ALA SEQRES 22 A 294 THR SER LEU SER GLU ASP PHE ASP LYS GLN LEU ALA LYS SEQRES 23 A 294 GLN THR ALA ALA LEU GLU LYS LYS SEQRES 1 B 294 MET ARG ARG LEU THR ALA ALA LEU CYS ALA LEU THR LEU SEQRES 2 B 294 LEU SER THR GLY ALA GLN ALA GLN THR ILE LYS ASP PHE SEQRES 3 B 294 LEU ALA VAL ALA MET LYS LYS TRP THR ALA PRO PHE GLU SEQRES 4 B 294 PRO PHE GLN LEU ILE ASP ASN ILE TYR TYR VAL GLY THR SEQRES 5 B 294 ASP GLY ILE ALA VAL TYR VAL ILE LYS THR SER GLN GLY SEQRES 6 B 294 LEU ILE LEU MET ASP THR ALA MET PRO GLN SER THR GLY SEQRES 7 B 294 MET ILE LYS ASP ASN ILE ALA LYS LEU GLY PHE LYS VAL SEQRES 8 B 294 ALA ASP ILE LYS LEU ILE LEU ASN THR HIS ALA HIS LEU SEQRES 9 B 294 ASP HIS THR GLY GLY PHE ALA GLU ILE LYS LYS GLU THR SEQRES 10 B 294 GLY ALA GLN LEU VAL ALA GLY GLU ARG ASP LYS PRO LEU SEQRES 11 B 294 LEU GLU GLY GLY TYR TYR PRO GLY ASP GLU LYS ASN GLU SEQRES 12 B 294 ASP LEU ALA PHE PRO ALA VAL LYS VAL ASP ARG ALA VAL SEQRES 13 B 294 LYS GLU GLY ASP ARG VAL THR LEU GLY ASP THR THR LEU SEQRES 14 B 294 THR ALA HIS ALA THR PRO GLY HIS SER PRO GLY CYS THR SEQRES 15 B 294 SER TRP GLU MET THR VAL LYS ASP GLY LYS GLU ASP ARG SEQRES 16 B 294 GLU VAL LEU PHE PHE CYS SER GLY THR VAL ALA LEU ASN SEQRES 17 B 294 ARG LEU VAL GLY GLN PRO THR TYR ALA GLY ILE VAL ASP SEQRES 18 B 294 ASP TYR ARG ALA THR PHE ALA LYS ALA LYS ALA MET LYS SEQRES 19 B 294 ILE ASP VAL LEU LEU GLY PRO HIS PRO GLU VAL TYR GLY SEQRES 20 B 294 MET GLN ALA LYS ARG ALA GLU MET LYS ASP GLY ALA PRO SEQRES 21 B 294 ASN PRO PHE ILE LYS PRO GLY GLU LEU VAL THR TYR ALA SEQRES 22 B 294 THR SER LEU SER GLU ASP PHE ASP LYS GLN LEU ALA LYS SEQRES 23 B 294 GLN THR ALA ALA LEU GLU LYS LYS HET ZN A 295 1 HET ZN A 296 1 HET ZN A 297 1 HET ZN B 295 1 HET ZN B 296 1 HET ZN B 297 1 HETNAM ZN ZINC ION FORMUL 3 ZN 6(ZN 2+) FORMUL 9 HOH *482(H2 O) HELIX 1 1 ILE A 23 MET A 31 1 9 HELIX 2 2 LYS A 32 ALA A 36 5 5 HELIX 3 3 MET A 73 GLN A 75 5 3 HELIX 4 4 SER A 76 LEU A 87 1 12 HELIX 5 5 LYS A 90 ALA A 92 5 3 HELIX 6 6 HIS A 103 GLY A 108 1 6 HELIX 7 7 GLY A 109 GLY A 118 1 10 HELIX 8 8 ASP A 127 GLY A 134 1 8 HELIX 9 9 ASN A 142 ALA A 146 5 5 HELIX 10 10 GLY A 218 MET A 233 1 16 HELIX 11 11 HIS A 242 TYR A 246 5 5 HELIX 12 12 GLY A 247 MET A 255 1 9 HELIX 13 13 GLY A 267 LEU A 291 1 25 HELIX 14 14 THR B 22 MET B 31 1 10 HELIX 15 15 LYS B 32 ALA B 36 5 5 HELIX 16 16 MET B 73 GLN B 75 5 3 HELIX 17 17 SER B 76 LEU B 87 1 12 HELIX 18 18 LYS B 90 ALA B 92 5 3 HELIX 19 19 HIS B 103 GLY B 108 1 6 HELIX 20 20 GLY B 109 GLY B 118 1 10 HELIX 21 21 ASP B 127 GLY B 134 1 8 HELIX 22 22 ASN B 142 ALA B 146 5 5 HELIX 23 23 GLY B 218 MET B 233 1 16 HELIX 24 24 HIS B 242 TYR B 246 5 5 HELIX 25 25 GLY B 247 MET B 255 1 9 HELIX 26 26 GLY B 267 ALA B 290 1 24 SHEET 1 A 7 PHE A 41 ILE A 44 0 SHEET 2 A 7 ILE A 47 TYR A 49 -1 O TYR A 49 N PHE A 41 SHEET 3 A 7 TYR A 58 THR A 62 -1 O VAL A 59 N TYR A 48 SHEET 4 A 7 GLY A 65 MET A 69 -1 O MET A 69 N TYR A 58 SHEET 5 A 7 ILE A 94 LEU A 98 1 O LYS A 95 N LEU A 66 SHEET 6 A 7 GLN A 120 GLY A 124 1 O VAL A 122 N ILE A 97 SHEET 7 A 7 ARG A 154 VAL A 156 1 O VAL A 156 N ALA A 123 SHEET 1 B 5 ARG A 161 LEU A 164 0 SHEET 2 B 5 THR A 167 ALA A 173 -1 O LEU A 169 N VAL A 162 SHEET 3 B 5 THR A 182 ASP A 190 -1 O GLU A 185 N THR A 170 SHEET 4 B 5 GLU A 193 PHE A 199 -1 O PHE A 199 N TRP A 184 SHEET 5 B 5 VAL A 237 LEU A 239 1 O LEU A 239 N LEU A 198 SHEET 1 C 7 PHE B 41 ILE B 44 0 SHEET 2 C 7 ILE B 47 TYR B 49 -1 O TYR B 49 N PHE B 41 SHEET 3 C 7 TYR B 58 THR B 62 -1 O VAL B 59 N TYR B 48 SHEET 4 C 7 GLY B 65 MET B 69 -1 O MET B 69 N TYR B 58 SHEET 5 C 7 ILE B 94 LEU B 98 1 O LEU B 98 N LEU B 68 SHEET 6 C 7 GLN B 120 GLY B 124 1 O GLN B 120 N ILE B 97 SHEET 7 C 7 ARG B 154 VAL B 156 1 O VAL B 156 N ALA B 123 SHEET 1 D 5 ARG B 161 LEU B 164 0 SHEET 2 D 5 THR B 167 ALA B 173 -1 O LEU B 169 N VAL B 162 SHEET 3 D 5 THR B 182 ASP B 190 -1 O SER B 183 N HIS B 172 SHEET 4 D 5 GLU B 193 PHE B 199 -1 O VAL B 197 N MET B 186 SHEET 5 D 5 VAL B 237 LEU B 239 1 O LEU B 239 N LEU B 198 SSBOND 1 CYS A 181 CYS A 201 1555 1555 2.12 SSBOND 2 CYS B 181 CYS B 201 1555 1555 2.15 LINK OE2 GLU B 158 ZN ZN B 297 1555 1555 1.95 LINK NE2 HIS B 177 ZN ZN B 296 1555 1555 1.97 LINK OE2 GLU A 158 ZN ZN A 297 1555 1555 1.99 LINK NZ LYS A 229 ZN ZN A 297 1555 1555 2.02 LINK NE2 HIS A 177 ZN ZN A 295 1555 1555 2.03 LINK NZ LYS B 229 ZN ZN B 297 1555 1555 2.04 LINK NE2 HIS A 242 ZN ZN A 296 1555 1555 2.05 LINK OD2 ASP A 105 ZN ZN A 296 1555 1555 2.06 LINK NE2 HIS A 101 ZN ZN A 295 1555 1555 2.06 LINK ND1 HIS A 172 ZN ZN A 297 1555 1555 2.07 LINK NE2 HIS A 106 ZN ZN A 296 1555 1555 2.07 LINK NE2 HIS B 101 ZN ZN B 296 1555 1555 2.07 LINK ND1 HIS A 103 ZN ZN A 295 1555 1555 2.08 LINK NE2 HIS B 242 ZN ZN B 295 1555 1555 2.08 LINK NE2 HIS B 106 ZN ZN B 295 1555 1555 2.09 LINK OD2 ASP B 105 ZN ZN B 295 1555 1555 2.09 LINK ND1 HIS B 172 ZN ZN B 297 1555 1555 2.11 LINK ND1 HIS B 103 ZN ZN B 296 1555 1555 2.11 LINK ZN ZN A 295 O HOH A 302 1555 1555 1.94 LINK ZN ZN B 295 O HOH B 482 1555 1555 1.96 LINK ZN ZN B 296 O HOH B 482 1555 1555 1.99 LINK ZN ZN A 296 O HOH A 302 1555 1555 2.06 LINK ZN ZN B 295 O HOH B 298 1555 1555 2.45 LINK ZN ZN A 296 O HOH A 299 1555 1555 2.53 SITE 1 AC1 5 HIS A 101 HIS A 103 HIS A 177 ZN A 296 SITE 2 AC1 5 HOH A 302 SITE 1 AC2 6 ASP A 105 HIS A 106 HIS A 242 ZN A 295 SITE 2 AC2 6 HOH A 299 HOH A 302 SITE 1 AC3 4 GLU A 158 HIS A 172 LYS A 229 LYS A 294 SITE 1 AC4 6 ASP B 105 HIS B 106 HIS B 242 ZN B 296 SITE 2 AC4 6 HOH B 298 HOH B 482 SITE 1 AC5 5 HIS B 101 HIS B 103 HIS B 177 ZN B 295 SITE 2 AC5 5 HOH B 482 SITE 1 AC6 4 GLU B 158 HIS B 172 LYS B 229 LYS B 294 CRYST1 42.501 44.773 76.966 78.92 89.51 61.91 P 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 0.023529 -0.012560 0.002539 0.00000 SCALE2 0.000000 0.025318 -0.005530 0.00000 SCALE3 0.000000 0.000000 0.013299 0.00000