HEADER HYDROLASE 20-APR-07 2UYX TITLE METALLO-BETA-LACTAMASE (1BC2) SINGLE POINT MUTANT D120S COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE II; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 30-257; COMPND 5 SYNONYM: METALLO-BETA-LACTAMASE, PENICILLINASE, CEPHALOSPORINASE; COMPND 6 EC: 3.5.2.6; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 STRAIN: 569/H/9; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: JM109 KEYWDS HYDROLASE, PENICILLINASE, METAL-BINDING, ANTIBIOTIC RESISTANCE, KEYWDS 2 METALLO BETA- LACTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR L.I.LARRULL,S.M.FABIANE,J.M.KOWALSKI,B.BENNETT,B.J.SUTTON,A.J.VILA REVDAT 6 13-DEC-23 2UYX 1 LINK REVDAT 5 19-DEC-18 2UYX 1 JRNL REMARK LINK ATOM REVDAT 4 13-JUL-11 2UYX 1 VERSN REVDAT 3 24-FEB-09 2UYX 1 VERSN REVDAT 2 09-OCT-07 2UYX 1 JRNL REVDAT 1 08-MAY-07 2UYX 0 JRNL AUTH L.I.LLARRULL,S.M.FABIANE,J.M.KOWALSKI,B.BENNETT,B.J.SUTTON, JRNL AUTH 2 A.J.VILA JRNL TITL ASP-120 LOCATES ZN2 FOR OPTIMAL METALLO-BETA-LACTAMASE JRNL TITL 2 ACTIVITY. JRNL REF J. BIOL. CHEM. V. 282 18276 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17426028 JRNL DOI 10.1074/JBC.M700742200 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15738 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 842 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1138 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1680 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1681 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : 1.41000 REMARK 3 B33 (A**2) : -1.43000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.57000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.147 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.272 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 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): 1734 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2342 ; 1.366 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 218 ; 6.044 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 67 ;40.535 ;25.672 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 319 ;14.287 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;14.461 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 278 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1232 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 818 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1160 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 222 ; 0.183 ; 0.200 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): 41 ; 0.226 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.247 ; 0.200 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): 1101 ; 0.692 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1745 ; 1.095 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 703 ; 2.027 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 596 ; 3.225 ; 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 32 A 106 REMARK 3 ORIGIN FOR THE GROUP (A): 11.0499 8.1000 61.5682 REMARK 3 T TENSOR REMARK 3 T11: -0.0935 T22: -0.0073 REMARK 3 T33: -0.1240 T12: 0.0687 REMARK 3 T13: 0.0032 T23: -0.0491 REMARK 3 L TENSOR REMARK 3 L11: 3.3447 L22: 3.4547 REMARK 3 L33: 5.0187 L12: 0.3129 REMARK 3 L13: 0.8927 L23: 0.3269 REMARK 3 S TENSOR REMARK 3 S11: -0.0086 S12: -0.2410 S13: 0.2790 REMARK 3 S21: 0.0782 S22: -0.1259 S23: 0.3952 REMARK 3 S31: -0.4422 S32: -0.8195 S33: 0.1345 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 107 A 135 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3842 6.8659 56.7672 REMARK 3 T TENSOR REMARK 3 T11: -0.1334 T22: -0.1912 REMARK 3 T33: -0.1525 T12: 0.0135 REMARK 3 T13: 0.0073 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 0.7218 L22: 0.6786 REMARK 3 L33: 12.7800 L12: 0.6999 REMARK 3 L13: 0.7805 L23: 0.7798 REMARK 3 S TENSOR REMARK 3 S11: -0.0862 S12: -0.1108 S13: 0.2056 REMARK 3 S21: -0.0989 S22: -0.1372 S23: -0.1076 REMARK 3 S31: -0.5480 S32: 0.0599 S33: 0.2233 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 136 A 291 REMARK 3 ORIGIN FOR THE GROUP (A): 13.3810 -0.6673 44.9025 REMARK 3 T TENSOR REMARK 3 T11: -0.1826 T22: -0.2172 REMARK 3 T33: -0.1546 T12: -0.0132 REMARK 3 T13: 0.0217 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 3.3157 L22: 1.2252 REMARK 3 L33: 4.6057 L12: 0.1798 REMARK 3 L13: 0.9163 L23: -0.1242 REMARK 3 S TENSOR REMARK 3 S11: -0.0455 S12: 0.0049 S13: 0.0380 REMARK 3 S21: 0.0141 S22: 0.0228 S23: 0.0688 REMARK 3 S31: 0.1480 S32: -0.2697 S33: 0.0228 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. N-TERMINUS AND RESIDUES 61-65 DISORDERED REMARK 4 REMARK 4 2UYX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-APR-07. REMARK 100 THE DEPOSITION ID IS D_1290032311. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-04 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 : SRS REMARK 200 BEAMLINE : PX14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.985 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS 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 : 16580 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 31.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3BC2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG 3350, 0.1M NA CACODYLATE PH REMARK 280 5.5, 0.1M NA TARTRATE, 25% GLYCEROL ADDED AS CRYOPROTECTANT REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 26.69450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.98500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.69450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.98500 REMARK 290 SMTRY3 4 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: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 120 TO SER 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 ALA A 26 REMARK 465 SER A 27 REMARK 465 GLN A 28 REMARK 465 LYS A 29 REMARK 465 VAL A 30 REMARK 465 GLU A 31 REMARK 465 PHE A 61 REMARK 465 ASN A 62 REMARK 465 GLY A 63 REMARK 465 GLU A 64 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 32 CG CD CE NZ 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 ND2 ASN A 240 O HOH A 2223 2.08 REMARK 500 O HOH A 2219 O HOH A 2221 2.16 REMARK 500 O HOH A 2033 O HOH A 2050 2.17 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 84 146.77 74.01 REMARK 500 SER A 85 -130.12 -92.95 REMARK 500 ALA A 117 45.97 -90.08 REMARK 500 ASP A 279 -161.61 -129.78 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 A2021 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A2039 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A2043 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH A2048 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A2049 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A2067 DISTANCE = 6.03 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 A1296 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 116 NE2 REMARK 620 2 HIS A 118 ND1 102.6 REMARK 620 3 HIS A 196 NE2 101.9 106.3 REMARK 620 4 GOL A1293 O3 111.0 118.1 115.0 REMARK 620 5 HOH A2281 O 108.5 111.9 123.3 8.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1297 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 221 SG REMARK 620 2 HIS A 263 NE2 114.6 REMARK 620 3 HOH A2280 O 83.9 77.8 REMARK 620 4 HOH A2283 O 114.2 108.1 154.2 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 GOL A1292 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1297 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BC2 RELATED DB: PDB REMARK 900 ZN-DEPENDENT METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS REMARK 900 RELATED ID: 1BMC RELATED DB: PDB REMARK 900 STRUCTURE OF A ZINC METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS REMARK 900 RELATED ID: 1BVT RELATED DB: PDB REMARK 900 METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS 569/H/9 REMARK 900 RELATED ID: 1DXK RELATED DB: PDB REMARK 900 METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS 569/H/9 C168S MUTANT REMARK 900 RELATED ID: 1MQO RELATED DB: PDB REMARK 900 METALLO-BETA-LACTAMASE BCII CD SUBSTITUTED FROM BACILLUSCEREUS AT REMARK 900 1.35 ANGSTROMS RESOLUTION REMARK 900 RELATED ID: 2BC2 RELATED DB: PDB REMARK 900 METALLO BETA-LACTAMASE II FROM BACILLUS CEREUS 569/H/9 AT PH 6.0, REMARK 900 TRIGONAL CRYSTAL FORM REMARK 900 RELATED ID: 2BFK RELATED DB: PDB REMARK 900 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS REMARK 900 MUTANT. SOLVED AT PH7 USING 20MM ZNSO4 IN BUFFER. 1MM DTT WAS USED REMARK 900 AS A REDUCING AGENT REMARK 900 RELATED ID: 2BFL RELATED DB: PDB REMARK 900 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS REMARK 900 MUTANT. SOLVED AT PH5 USING 20MM ZNSO4 IN BUFFER. 1MM DTT WAS USED REMARK 900 AS A REDUCING AGENT. REMARK 900 RELATED ID: 2BFZ RELATED DB: PDB REMARK 900 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS REMARK 900 MUTANT. SOLVED AT PH4.5 USING 20MM ZNSO4 IN BUFFER. 1MM DTT WAS REMARK 900 USED AS A REDUCING AGENT. CYS221 IS OXIDIZED. REMARK 900 RELATED ID: 2BG2 RELATED DB: PDB REMARK 900 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS REMARK 900 MUTANT. SOLVED AT PH4.5 USING 20MM ZNSO4 IN THE BUFFER. 1MM DTT AND REMARK 900 1MM TCEP-HCL WERE USED AS REDUCING AGENTS. CYS221 IS REDUCED. REMARK 900 RELATED ID: 2BG6 RELATED DB: PDB REMARK 900 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS REMARK 900 MUTANT. SOLVED AT PH5 USING 20 MICROMOLAR ZNSO4 IN THE BUFFER. 1MM REMARK 900 DTT WAS USED AS A REDUCING AGENT. CYS221 IS OXIDIZED. REMARK 900 RELATED ID: 2BG7 RELATED DB: PDB REMARK 900 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS REMARK 900 MUTANT. SOLVED AT PH4.5 USING 20 MICROMOLAR ZNSO4 IN THE BUFFER. REMARK 900 1MM DTT WAS USED AS A REDUCING AGENT. CYS221 IS OXIDIZED. REMARK 900 RELATED ID: 2BG8 RELATED DB: PDB REMARK 900 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS REMARK 900 MUTANT. SOLVED AT PH4.5 USING 20 MICROMOLAR ZNSO4 IN THE BUFFER. REMARK 900 1MM DTT AND 1MM TCEP-HCL WERE USED AS REDUCING AGENTS. REMARK 900 RELATED ID: 2BGA RELATED DB: PDB REMARK 900 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS REMARK 900 MUTANT. SOLVED AT PH7 USING 20 MICROMOLAR ZNSO4 IN THE BUFFER. 1MM REMARK 900 DTT WAS USED AS A REDUCING AGENT. CYS221 IS OXIDIZED. REMARK 900 RELATED ID: 3BC2 RELATED DB: PDB REMARK 900 METALLO BETA-LACTAMASE II FROM BACILLUS CEREUS 569/H/9 AT PH 6.0, REMARK 900 MONOCLINIC CRYSTAL FORM REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINUS DISORDERED, LOOP DISORDERED DBREF 2UYX A 26 45 UNP P04190 BLA2_BACCE 30 49 DBREF 2UYX A 47 64 UNP P04190 BLA2_BACCE 50 67 DBREF 2UYX A 66 100 UNP P04190 BLA2_BACCE 68 102 DBREF 2UYX A 102 107 UNP P04190 BLA2_BACCE 103 108 DBREF 2UYX A 109 131 UNP P04190 BLA2_BACCE 109 131 DBREF 2UYX A 133 150 UNP P04190 BLA2_BACCE 132 149 DBREF 2UYX A 167 205 UNP P04190 BLA2_BACCE 150 188 DBREF 2UYX A 209 211 UNP P04190 BLA2_BACCE 189 191 DBREF 2UYX A 215 265 UNP P04190 BLA2_BACCE 192 242 DBREF 2UYX A 277 291 UNP P04190 BLA2_BACCE 243 257 SEQADV 2UYX SER A 120 UNP P04190 ASP 120 ENGINEERED MUTATION SEQRES 1 A 228 ALA SER GLN LYS VAL GLU LYS THR VAL ILE LYS ASN GLU SEQRES 2 A 228 THR GLY THR ILE SER ILE SER GLN LEU ASN LYS ASN VAL SEQRES 3 A 228 TRP VAL HIS THR GLU LEU GLY SER PHE ASN GLY GLU ALA SEQRES 4 A 228 VAL PRO SER ASN GLY LEU VAL LEU ASN THR SER LYS GLY SEQRES 5 A 228 LEU VAL LEU VAL ASP SER SER TRP ASP ASP LYS LEU THR SEQRES 6 A 228 LYS GLU LEU ILE GLU MET VAL GLU LYS LYS PHE GLN LYS SEQRES 7 A 228 ARG VAL THR ASP VAL ILE ILE THR HIS ALA HIS ALA SER SEQRES 8 A 228 ARG ILE GLY GLY ILE LYS THR LEU LYS GLU ARG GLY ILE SEQRES 9 A 228 LYS ALA HIS SER THR ALA LEU THR ALA GLU LEU ALA LYS SEQRES 10 A 228 LYS ASN GLY TYR GLU GLU PRO LEU GLY ASP LEU GLN THR SEQRES 11 A 228 VAL THR ASN LEU LYS PHE GLY ASN MET LYS VAL GLU THR SEQRES 12 A 228 PHE TYR PRO GLY LYS GLY HIS THR GLU ASP ASN ILE VAL SEQRES 13 A 228 VAL TRP LEU PRO GLN TYR ASN ILE LEU VAL GLY GLY CYS SEQRES 14 A 228 LEU VAL LYS SER THR SER ALA LYS ASP LEU GLY ASN VAL SEQRES 15 A 228 ALA ASP ALA TYR VAL ASN GLU TRP SER THR SER ILE GLU SEQRES 16 A 228 ASN VAL LEU LYS ARG TYR ARG ASN ILE ASN ALA VAL VAL SEQRES 17 A 228 PRO GLY HIS GLY GLU VAL GLY ASP LYS GLY LEU LEU LEU SEQRES 18 A 228 HIS THR LEU ASP LEU LEU LYS HET GOL A1292 6 HET GOL A1293 6 HET GOL A1294 6 HET GOL A1295 6 HET ZN A1296 1 HET ZN A1297 1 HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 4(C3 H8 O3) FORMUL 6 ZN 2(ZN 2+) FORMUL 8 HOH *283(H2 O) HELIX 1 1 ASP A 88 GLN A 105 1 17 HELIX 2 2 HIS A 118 GLY A 123 1 6 HELIX 3 3 GLY A 124 ARG A 131 1 8 HELIX 4 4 THR A 139 ASN A 149 1 11 HELIX 5 5 CYS A 221 VAL A 223 5 3 HELIX 6 6 TYR A 238 TYR A 253 1 16 HELIX 7 7 LYS A 280 LEU A 290 1 11 SHEET 1 AA 7 VAL A 34 LYS A 36 0 SHEET 2 AA 7 ILE A 42 ASN A 49 -1 O ILE A 44 N ILE A 35 SHEET 3 AA 7 VAL A 52 GLY A 59 -1 O VAL A 52 N LEU A 48 SHEET 4 AA 7 VAL A 67 THR A 76 -1 O VAL A 67 N GLY A 59 SHEET 5 AA 7 GLY A 79 VAL A 83 -1 O GLY A 79 N THR A 76 SHEET 6 AA 7 VAL A 109 ILE A 113 1 N THR A 110 O LEU A 80 SHEET 7 AA 7 LYS A 135 HIS A 137 1 O LYS A 135 N VAL A 112 SHEET 1 AB 5 VAL A 177 PHE A 182 0 SHEET 2 AB 5 MET A 185 PHE A 190 -1 O MET A 185 N PHE A 182 SHEET 3 AB 5 VAL A 202 TRP A 204 -1 O VAL A 202 N PHE A 190 SHEET 4 AB 5 ILE A 216 GLY A 220 -1 O VAL A 218 N VAL A 203 SHEET 5 AB 5 ALA A 258 PRO A 261 1 O ALA A 258 N LEU A 217 LINK NE2 HIS A 116 ZN ZN A1296 1555 1555 2.16 LINK ND1 HIS A 118 ZN ZN A1296 1555 1555 2.03 LINK NE2 HIS A 196 ZN ZN A1296 1555 1555 2.01 LINK SG CYS A 221 ZN ZN A1297 1555 1555 2.21 LINK NE2 HIS A 263 ZN ZN A1297 1555 1555 2.09 LINK O3 BGOL A1293 ZN ZN A1296 1555 1555 2.55 LINK ZN ZN A1296 O HOH A2281 1555 1555 2.24 LINK ZN ZN A1297 O HOH A2280 1555 1555 2.20 LINK ZN ZN A1297 O HOH A2283 1555 1555 2.33 SITE 1 AC1 11 HIS A 118 SER A 120 HIS A 196 GOL A1293 SITE 2 AC1 11 ZN A1296 ZN A1297 HOH A2277 HOH A2278 SITE 3 AC1 11 HOH A2279 HOH A2280 HOH A2281 SITE 1 AC2 11 HIS A 118 ALA A 119 SER A 120 CYS A 221 SITE 2 AC2 11 GOL A1292 ZN A1296 ZN A1297 HOH A2277 SITE 3 AC2 11 HOH A2279 HOH A2280 HOH A2281 SITE 1 AC3 6 ALA A 117 HIS A 118 ASN A 149 THR A 197 SITE 2 AC3 6 ASP A 199 ASP A 236 SITE 1 AC4 4 GLU A 97 GLU A 130 ARG A 131 HOH A2077 SITE 1 AC5 6 HIS A 116 HIS A 118 HIS A 196 GOL A1292 SITE 2 AC5 6 GOL A1293 HOH A2281 SITE 1 AC6 6 CYS A 221 HIS A 263 GOL A1292 GOL A1293 SITE 2 AC6 6 HOH A2280 HOH A2283 CRYST1 53.389 61.970 69.573 90.00 93.28 90.00 C 1 2 1 4 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 0.018730 0.000000 0.001073 0.00000 SCALE2 0.000000 0.016137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014397 0.00000