HEADER HYDROLASE/HYDROLASE INHIBITOR 20-FEB-13 2M5D TITLE SOLUTION STRUCTURE OF THE BACILLUS CEREUS METALLO-BETA-LACTAMASE BCII TITLE 2 IN COMPLEX WITH R-THIOMANDELIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BCII, BETA-LACTAMASE II, CEPHALOSPORINASE, PENICILLINASE; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 STRAIN: 569/H; SOURCE 5 GENE: BLM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET9A/BCII KEYWDS BCII, METALLO-BETA-LACTAMASE, R-THIOMANDELIC ACID, KEYWDS 2 MERCAPTOCARBOXYLATE INHIBITOR, BROAD SPECTRUM INHIBITOR, HYDROLASE- KEYWDS 3 HYDROLASE INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.I.KARSISIOTIS,C.F.DAMBLON,G.C.K.ROBERTS REVDAT 1 09-OCT-13 2M5D 0 JRNL AUTH A.I.KARSISIOTIS,C.F.DAMBLON,G.C.K.ROBERTS JRNL TITL SOLUTION STRUCTURES OF THE BACILLUS CEREUS JRNL TITL 2 METALLO-BETA-LACTAMASE BCII AND ITS COMPLEX WITH THE BROAD JRNL TITL 3 SPECTRUM INHIBITOR R-THIOMANDELIC ACID JRNL REF BIOCHEM.J. 2013 JRNL REFN ESSN 1470-8728 JRNL PMID 24059435 JRNL DOI 10.1042/BJ20131003 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.I.KARSISIOTIS,C.F.DAMBLON,G.C.K.ROBERTS REMARK 1 TITL COMPLETE (1)H, (15)N AND (13)C RESONANCE ASSIGNMENTS OF REMARK 1 TITL 2 BACILLUS CEREUS METALLO-BETA-LACTAMASE AND ITS COMPLEX WITH REMARK 1 TITL 3 THE INHIBITOR R-THIOMANDELIC ACID REMARK 1 REF BIOMOL.NMR ASSIGN. 2013 REMARK 1 REFN ESSN 1874-270X REMARK 1 PMID 23838816 REMARK 1 DOI 10.1007/S12104-013-9507-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE REFINEMENT PROTOCOL USED CONSISTED REMARK 3 OF FIVE CYCLES OF SIMULATED ANNEALING WITH A HIGH START REMARK 3 TEMPERATURE (8000 K) AND A GRADUAL SLOW COOLING TO A LOW REMARK 3 TEMPERATURE (100 K) IN A LARGE NUMBER OF STEPS (20,000). THIS REMARK 3 STANDARD TORSION ANGLE BASED SIMULATING ANNEALING PROTOCOL WITH REMARK 3 ALL CONSTRAINTS APPLIED SIMULTANEOUSLY IS COMBINED WITH CYCLES OF REMARK 3 REDUNDANT DIHEDRAL ANGLE CONSTRAINTS (REDAC; GUNTERT AND REMARK 3 WUTHRICH, 1991). SEVERAL CYCLES OF THIS COMBINED REFINEMENT REMARK 3 PROTOCOL, WHICH ELIMINATES VIOLATIONS AND PROGRESSIVELY REDUCES REMARK 3 TARGET FUNCTION VALUES WHILE IMPROVING LOCAL AND OVERALL QUALITY, REMARK 3 WERE USED TO GENERATE THE FINAL CONVERGED STRUCTURES. OUT OF AN REMARK 3 ENSEMBLE OF 100 CONVERGED STRUCTURES GENERATED, THE 20 BEST REMARK 3 (LOWEST CYANA TARGET FUNCTION DURING REFINEMENT) STRUCTURES WERE REMARK 3 SELECTED. REMARK 4 REMARK 4 2M5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-FEB-13. REMARK 100 THE RCSB ID CODE IS RCSB103229. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 15N] BCII-1, 1 MM R- REMARK 210 THIOMANDELIC ACID-2, 20 MM MES-3, REMARK 210 100 MM SODIUM CHLORIDE-4, 90% REMARK 210 H2O/10% D2O; 1 MM [U-99% 13C; U- REMARK 210 99% 15N] BCII-5, 1 MM R- REMARK 210 THIOMANDELIC ACID-6, 20 MM MES-7, REMARK 210 100 MM SODIUM CHLORIDE-8, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HN(CA)CO; 3D HNCO; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, CANDID, SPARKY, MOLMOL, REMARK 210 NMRPIPE, TOPSPIN, XWINNMR, REMARK 210 PROCHECKNMR, WHATIF, NMRDRAW REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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: CLOSE CONTACTS 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 HE2 HIS A 149 ZN ZN A 301 1.35 REMARK 500 HE2 HIS A 86 ZN ZN A 301 1.60 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 1 LYS A 3 84.95 55.96 REMARK 500 1 GLU A 5 57.91 -106.10 REMARK 500 1 VAL A 8 97.68 61.08 REMARK 500 1 PHE A 34 122.41 -172.19 REMARK 500 1 ASN A 47 74.82 -106.34 REMARK 500 1 LYS A 50 24.69 -155.60 REMARK 500 1 ASP A 56 132.21 179.23 REMARK 500 1 SER A 57 -167.08 -71.34 REMARK 500 1 GLU A 72 49.95 -86.71 REMARK 500 1 LYS A 73 -42.13 -145.43 REMARK 500 1 GLN A 76 46.63 32.92 REMARK 500 1 ARG A 91 -52.62 -123.83 REMARK 500 1 SER A 107 163.86 179.50 REMARK 500 1 TYR A 120 -173.35 -59.60 REMARK 500 1 GLU A 122 122.84 65.69 REMARK 500 1 PRO A 123 -170.52 -69.73 REMARK 500 1 ASP A 126 51.23 -152.75 REMARK 500 1 PHE A 143 136.76 -171.98 REMARK 500 1 PRO A 159 72.18 -69.85 REMARK 500 1 GLN A 160 -34.24 179.47 REMARK 500 1 ASN A 202 21.36 -152.40 REMARK 500 1 PRO A 208 -170.27 -69.71 REMARK 500 2 VAL A 4 145.12 -176.22 REMARK 500 2 VAL A 8 94.06 60.54 REMARK 500 2 SER A 19 134.64 -173.45 REMARK 500 2 LYS A 23 -76.86 68.00 REMARK 500 2 ASN A 35 34.07 -171.31 REMARK 500 2 ASN A 47 48.18 -93.33 REMARK 500 2 SER A 49 34.17 -95.99 REMARK 500 2 LYS A 50 28.95 -157.65 REMARK 500 2 ASP A 56 132.60 -179.72 REMARK 500 2 SER A 57 -169.04 -71.24 REMARK 500 2 LYS A 73 -41.36 -140.14 REMARK 500 2 GLN A 76 46.74 32.96 REMARK 500 2 ARG A 91 -52.36 -128.12 REMARK 500 2 SER A 107 159.32 179.21 REMARK 500 2 TYR A 120 -173.12 -59.53 REMARK 500 2 GLU A 122 125.15 66.07 REMARK 500 2 PRO A 123 -170.60 -69.80 REMARK 500 2 THR A 129 -70.13 -50.97 REMARK 500 2 ASN A 132 96.18 -66.14 REMARK 500 2 PHE A 143 137.93 -175.49 REMARK 500 2 PRO A 159 72.89 -69.79 REMARK 500 2 GLN A 160 -34.14 179.31 REMARK 500 2 PRO A 208 -172.25 -69.77 REMARK 500 3 VAL A 4 143.02 -175.26 REMARK 500 3 GLU A 5 60.51 -108.42 REMARK 500 3 VAL A 8 94.76 60.79 REMARK 500 3 SER A 19 133.79 -174.49 REMARK 500 3 LYS A 23 -70.74 70.68 REMARK 500 REMARK 500 THIS ENTRY HAS 504 RAMACHANDRAN OUTLIERS. 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 1 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 149 NE2 REMARK 620 2 HIS A 88 ND1 79.1 REMARK 620 3 HIS A 86 NE2 96.1 96.6 REMARK 620 4 RTD A 303 S1 104.7 123.0 137.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 90 OD2 REMARK 620 2 RTD A 303 S1 89.0 REMARK 620 3 CYS A 168 SG 110.2 96.1 REMARK 620 4 HIS A 210 NE2 153.3 84.5 96.2 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 ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RTD A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19048 RELATED DB: BMRB REMARK 900 RELATED ID: 2M5C RELATED DB: PDB DBREF 2M5D A 1 227 UNP P04190 BLA2_BACCE 31 257 SEQRES 1 A 227 SER GLN LYS VAL GLU LYS THR VAL ILE LYS ASN GLU THR SEQRES 2 A 227 GLY THR ILE SER ILE SER GLN LEU ASN LYS ASN VAL TRP SEQRES 3 A 227 VAL HIS THR GLU LEU GLY SER PHE ASN GLY GLU ALA VAL SEQRES 4 A 227 PRO SER ASN GLY LEU VAL LEU ASN THR SER LYS GLY LEU SEQRES 5 A 227 VAL LEU VAL ASP SER SER TRP ASP ASP LYS LEU THR LYS SEQRES 6 A 227 GLU LEU ILE GLU MET VAL GLU LYS LYS PHE GLN LYS ARG SEQRES 7 A 227 VAL THR ASP VAL ILE ILE THR HIS ALA HIS ALA ASP ARG SEQRES 8 A 227 ILE GLY GLY ILE LYS THR LEU LYS GLU ARG GLY ILE LYS SEQRES 9 A 227 ALA HIS SER THR ALA LEU THR ALA GLU LEU ALA LYS LYS SEQRES 10 A 227 ASN GLY TYR GLU GLU PRO LEU GLY ASP LEU GLN THR VAL SEQRES 11 A 227 THR ASN LEU LYS PHE GLY ASN MET LYS VAL GLU THR PHE SEQRES 12 A 227 TYR PRO GLY LYS GLY HIS THR GLU ASP ASN ILE VAL VAL SEQRES 13 A 227 TRP LEU PRO GLN TYR ASN ILE LEU VAL GLY GLY CYS LEU SEQRES 14 A 227 VAL LYS SER THR SER ALA LYS ASP LEU GLY ASN VAL ALA SEQRES 15 A 227 ASP ALA TYR VAL ASN GLU TRP SER THR SER ILE GLU ASN SEQRES 16 A 227 VAL LEU LYS ARG TYR ARG ASN ILE ASN ALA VAL VAL PRO SEQRES 17 A 227 GLY HIS GLY GLU VAL GLY ASP LYS GLY LEU LEU LEU HIS SEQRES 18 A 227 THR LEU ASP LEU LEU LYS HET ZN A 301 1 HET ZN A 302 1 HET RTD A 303 17 HETNAM ZN ZINC ION HETNAM RTD (2R)-PHENYL(SULFANYL)ETHANOIC ACID HETSYN RTD ALPHA-MERCAPTOPHENYLACETIC ACID, R-THIOMANDELIC ACID FORMUL 2 ZN 2(ZN 2+) FORMUL 4 RTD C8 H8 O2 S HELIX 1 1 ASP A 60 PHE A 75 1 16 HELIX 2 2 HIS A 88 GLY A 93 1 6 HELIX 3 3 GLY A 94 LYS A 99 1 6 HELIX 4 4 THR A 108 GLY A 119 1 12 HELIX 5 5 TYR A 185 TYR A 200 1 16 HELIX 6 6 LYS A 216 LYS A 227 1 12 SHEET 1 A 4 VAL A 25 TRP A 26 0 SHEET 2 A 4 VAL A 45 LEU A 46 -1 O VAL A 45 N TRP A 26 SHEET 3 A 4 LEU A 52 LEU A 54 -1 O VAL A 53 N LEU A 46 SHEET 4 A 4 VAL A 79 VAL A 82 1 O ASP A 81 N LEU A 54 SHEET 1 B 2 GLU A 30 PHE A 34 0 SHEET 2 B 2 GLU A 37 SER A 41 -1 O GLU A 37 N PHE A 34 SHEET 1 C 3 ASN A 132 LEU A 133 0 SHEET 2 C 3 VAL A 140 PHE A 143 -1 O VAL A 140 N LEU A 133 SHEET 3 C 3 VAL A 155 TRP A 157 -1 O TRP A 157 N GLU A 141 SHEET 1 D 2 ILE A 163 GLY A 167 0 SHEET 2 D 2 ALA A 205 PRO A 208 1 O ALA A 205 N LEU A 164 LINK NE2 HIS A 149 ZN ZN A 301 1555 1555 2.27 LINK OD2 ASP A 90 ZN ZN A 302 1555 1555 2.40 LINK ZN ZN A 302 S1 RTD A 303 1555 1555 2.41 LINK SG CYS A 168 ZN ZN A 302 1555 1555 2.41 LINK ND1 HIS A 88 ZN ZN A 301 1555 1555 2.41 LINK NE2 HIS A 86 ZN ZN A 301 1555 1555 2.43 LINK ZN ZN A 301 S1 RTD A 303 1555 1555 2.43 LINK NE2 HIS A 210 ZN ZN A 302 1555 1555 2.50 SITE 1 AC1 7 HIS A 86 HIS A 88 ASP A 90 HIS A 149 SITE 2 AC1 7 CYS A 168 ZN A 302 RTD A 303 SITE 1 AC2 6 ASP A 90 ARG A 91 CYS A 168 HIS A 210 SITE 2 AC2 6 ZN A 301 RTD A 303 SITE 1 AC3 9 PHE A 34 VAL A 39 TRP A 59 ASP A 90 SITE 2 AC3 9 HIS A 149 CYS A 168 HIS A 210 ZN A 301 SITE 3 AC3 9 ZN A 302 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 221 0 3 6 11 0 7 6 0 0 0 18 END