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- PDB-4c09: Crystal structure of the metallo-beta-lactamase BCII -

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Basic information

Entry
Database: PDB / ID: 4c09
TitleCrystal structure of the metallo-beta-lactamase BCII
ComponentsBETA-LACTAMASE 2
KeywordsHYDROLASE / MBL / METALLO-BETA-LACTAMASE / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase ...: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsZollman, D. / Brem, J. / McDonough, M.A. / van Berkel, S.S. / Schofield, C.J.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2015
Title: Structural Basis of Metallo-beta-Lactamase Inhibition by Captopril Stereoisomers.
Authors: Brem, J. / van Berkel, S.S. / Zollman, D. / Lee, S.Y. / Gileadi, O. / McHugh, P.J. / Walsh, T.R. / McDonough, M.A. / Schofield, C.J.
History
DepositionJul 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Other / Structure summary
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Jan 13, 2016Group: Database references
Revision 1.4Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4086
Polymers24,9971
Non-polymers4115
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.300, 61.970, 69.460
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BETA-LACTAMASE 2 / BETA-LACTAMASE II / CEPHALOSPORINASE / PENICILLINASE / BCII


Mass: 24996.520 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: 569/H/9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P04190, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHROMOSOME DERIVED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 5.5
Details: 0.2 M AMMONIUM SULFATE, 0.1 M BIS TRIS, 25 % W/V PEG 3350 PH 5.5, 1 MM TCEP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→34.68 Å / Num. obs: 69108 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 14.14 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.1
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MQO

1mqo


Resolution: 1.2→34.681 Å / SU ML: 0.1 / σ(F): 1.18 / Phase error: 12.83 / Stereochemistry target values: ML
Details: CONFORMATION OF RAMACHANDRAN OUTLIERS 86 ASP, 87 SER, 245 ASP VALIDATED BY CLEAR ELECTRON DENSITY. POSSIBLE OXIDISED CYS 198 AT VERY LOW OCCUPANCY LEFT UNMODELED DUE TO LOW OCCUPANCY.
RfactorNum. reflection% reflection
Rfree0.1393 2007 2.9 %
Rwork0.1186 --
obs0.1192 69099 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→34.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 19 282 1999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141884
X-RAY DIFFRACTIONf_angle_d1.4332579
X-RAY DIFFRACTIONf_dihedral_angle_d13.248682
X-RAY DIFFRACTIONf_chiral_restr0.088300
X-RAY DIFFRACTIONf_plane_restr0.008331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.23431410.19984595X-RAY DIFFRACTION95
1.23-1.26330.20021290.1724696X-RAY DIFFRACTION96
1.2633-1.30050.17461560.14594741X-RAY DIFFRACTION97
1.3005-1.34240.16241280.12794767X-RAY DIFFRACTION98
1.3424-1.39040.1471480.11764765X-RAY DIFFRACTION98
1.3904-1.44610.14731520.10714810X-RAY DIFFRACTION99
1.4461-1.51190.12481470.09064832X-RAY DIFFRACTION99
1.5119-1.59160.12591350.08384793X-RAY DIFFRACTION99
1.5916-1.69130.11591500.0864854X-RAY DIFFRACTION99
1.6913-1.82190.13331440.09094845X-RAY DIFFRACTION99
1.8219-2.00520.11851400.09834820X-RAY DIFFRACTION99
2.0052-2.29530.13211480.10824838X-RAY DIFFRACTION99
2.2953-2.89170.14791470.12674839X-RAY DIFFRACTION98
2.8917-34.69560.13851420.13654897X-RAY DIFFRACTION98

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