HEADER HYDROLASE 24-MAY-18 6DJA TITLE ZN-DEPENDENT 5/B/6 METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE TYPE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 32-356; COMPND 5 SYNONYM: B2 METALLO-BETA-LACTAMASE,BETA-LACTAMASE II, COMPND 6 CEPHALOSPORINASE,METALLO-BETA-LACTAMASE TYPE II,METALLOTHIOPROTEIN COMPND 7 BETA-LACTAMASE II,PENICILLINASE,ZINC-REQUIRING BETA-LACTAMASE II; COMPND 8 EC: 3.5.2.6; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET29/BLA KEYWDS HYDROLASE, ZINC, LACTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR A.A.BUI,N.H.KHAN,R.W.SHAW,R.B.SUTTON REVDAT 3 11-OCT-23 6DJA 1 REMARK REVDAT 2 11-DEC-19 6DJA 1 JRNL REVDAT 1 29-MAY-19 6DJA 0 JRNL AUTH N.H.KHAN,A.A.BUI,Y.XIAO,R.B.SUTTON,R.W.SHAW,B.J.WYLIE, JRNL AUTH 2 M.P.LATHAM JRNL TITL A DNA APTAMER REVEALS AN ALLOSTERIC SITE FOR INHIBITION IN JRNL TITL 2 METALLO-BETA-LACTAMASES. JRNL REF PLOS ONE V. 14 14440 2019 JRNL REFN ESSN 1932-6203 JRNL PMID 31009467 JRNL DOI 10.1371/JOURNAL.PONE.0214440 REMARK 2 REMARK 2 RESOLUTION. 2.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 9331 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.959 REMARK 3 FREE R VALUE TEST SET COUNT : 1032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1721 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 68 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DJA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.282715 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10388 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 37.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 31.70 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 43.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 24.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34600 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: PHENIX REMARK 200 STARTING MODEL: 1BC2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 8000, 0.1M TRIS, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.12133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.06067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 32.06067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 64.12133 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 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 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 86 154.88 68.95 REMARK 500 SER A 87 -130.32 -99.56 REMARK 500 ALA A 117 58.04 -97.57 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 A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 116 NE2 REMARK 620 2 HIS A 118 ND1 101.8 REMARK 620 3 HIS A 179 NE2 104.1 108.3 REMARK 620 4 HOH A 428 O 104.3 134.1 101.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 198 SG REMARK 620 2 HIS A 240 NE2 129.4 REMARK 620 3 HOH A 428 O 93.6 95.1 REMARK 620 N 1 2 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 DBREF 6DJA A 36 257 UNP P14488 BLAB_BACCE 35 256 SEQRES 1 A 222 HIS LYS VAL ILE LYS ASN GLU THR GLY THR ILE SER ILE SEQRES 2 A 222 SER GLN LEU ASN LYS ASN VAL TRP VAL HIS THR GLU LEU SEQRES 3 A 222 GLY TYR PHE SER GLY GLU ALA VAL PRO SER ASN GLY LEU SEQRES 4 A 222 VAL LEU ASN THR SER LYS GLY LEU VAL LEU VAL ASP SER SEQRES 5 A 222 SER TRP ASP ASP LYS LEU THR LYS GLU LEU ILE GLU MET SEQRES 6 A 222 VAL GLU LYS LYS PHE LYS LYS ARG VAL THR ASP VAL ILE SEQRES 7 A 222 ILE THR HIS ALA HIS ALA ASP ARG ILE GLY GLY MET LYS SEQRES 8 A 222 THR LEU LYS GLU ARG GLY ILE LYS ALA HIS SER THR ALA SEQRES 9 A 222 LEU THR ALA GLU LEU ALA LYS LYS ASN GLY TYR GLU GLU SEQRES 10 A 222 PRO LEU GLY ASP LEU GLN SER VAL THR ASN LEU LYS PHE SEQRES 11 A 222 GLY ASN MET LYS VAL GLU THR PHE TYR PRO GLY LYS GLY SEQRES 12 A 222 HIS THR GLU ASP ASN ILE VAL VAL TRP LEU PRO GLN TYR SEQRES 13 A 222 GLN ILE LEU ALA GLY GLY CYS LEU VAL LYS SER ALA SER SEQRES 14 A 222 SER LYS ASP LEU GLY ASN VAL ALA ASP ALA TYR VAL ASN SEQRES 15 A 222 GLU TRP SER THR SER ILE GLU ASN VAL LEU LYS ARG TYR SEQRES 16 A 222 GLY ASN ILE ASN LEU VAL VAL PRO GLY HIS GLY GLU VAL SEQRES 17 A 222 GLY ASP ARG GLY LEU LEU LEU HIS THR LEU ASP LEU LEU SEQRES 18 A 222 LYS HET ZN A 301 1 HET ZN A 302 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *68(H2 O) HELIX 1 AA1 ASP A 90 LYS A 106 1 17 HELIX 2 AA2 HIS A 118 GLY A 123 1 6 HELIX 3 AA3 GLY A 124 ARG A 131 1 8 HELIX 4 AA4 THR A 138 ASN A 148 1 11 HELIX 5 AA5 CYS A 198 VAL A 200 5 3 HELIX 6 AA6 GLU A 218 TYR A 230 1 13 HELIX 7 AA7 ARG A 246 LYS A 257 1 12 SHEET 1 AA1 7 VAL A 38 LYS A 40 0 SHEET 2 AA1 7 ILE A 46 ASN A 52 -1 O ILE A 48 N ILE A 39 SHEET 3 AA1 7 VAL A 55 PHE A 64 -1 O VAL A 57 N SER A 49 SHEET 4 AA1 7 GLU A 67 THR A 78 -1 O VAL A 75 N TRP A 56 SHEET 5 AA1 7 GLY A 81 VAL A 85 -1 O VAL A 83 N LEU A 76 SHEET 6 AA1 7 VAL A 109 ILE A 113 1 O THR A 110 N LEU A 82 SHEET 7 AA1 7 LYS A 134 HIS A 136 1 O HIS A 136 N VAL A 112 SHEET 1 AA2 5 VAL A 160 PHE A 165 0 SHEET 2 AA2 5 MET A 168 PHE A 173 -1 O VAL A 170 N LEU A 163 SHEET 3 AA2 5 VAL A 185 LEU A 188 -1 O TRP A 187 N GLU A 171 SHEET 4 AA2 5 ILE A 193 GLY A 197 -1 O ALA A 195 N VAL A 186 SHEET 5 AA2 5 LEU A 235 PRO A 238 1 O VAL A 237 N LEU A 194 LINK NE2 HIS A 116 ZN ZN A 301 1555 1555 2.20 LINK ND1 HIS A 118 ZN ZN A 301 1555 1555 2.22 LINK NE2 HIS A 179 ZN ZN A 301 1555 1555 2.19 LINK SG CYS A 198 ZN ZN A 302 1555 1555 1.94 LINK NE2AHIS A 240 ZN ZN A 302 1555 1555 2.57 LINK ZN ZN A 301 O HOH A 428 1555 1555 2.48 LINK ZN ZN A 302 O HOH A 428 1555 1555 2.28 SITE 1 AC1 4 HIS A 116 HIS A 118 HIS A 179 HOH A 428 SITE 1 AC2 4 ASP A 120 CYS A 198 HIS A 240 HOH A 428 CRYST1 71.087 71.087 96.182 90.00 90.00 120.00 P 32 2 1 6 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 0.014067 0.008122 0.000000 0.00000 SCALE2 0.000000 0.016243 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010397 0.00000