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- PDB-1bvt: METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS 569/H/9 -

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Basic information

Entry
Database: PDB / ID: 1bvt
TitleMETALLO-BETA-LACTAMASE FROM BACILLUS CEREUS 569/H/9
ComponentsPROTEIN (BETA-LACTAMASE)
KeywordsHYDROLASE / HYDROLASE (BETA-LACTAMASE) / METALLO BETA-LACTAMASE / ZINC
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCarfi, A. / Duee, E. / Dideberg, O.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: 1.85 A resolution structure of the zinc (II) beta-lactamase from Bacillus cereus.
Authors: Carfi, A. / Duee, E. / Galleni, M. / Frere, J.M. / Dideberg, O.
#1: Journal: Embo J. / Year: 1995
Title: The 3-D Structure of a Zinc Metallo-Beta-Lactamase from Bacillus Cereus Reveals a New Type of Protein Fold
Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.M. / Dideberg, O.
History
DepositionSep 18, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 23, 1998Provider: repository / Type: Initial release
SupersessionApr 12, 2000ID: 1BME
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (BETA-LACTAMASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1874
Polymers24,9961
Non-polymers1923
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.000, 61.350, 69.450
Angle α, β, γ (deg.)90.00, 92.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (BETA-LACTAMASE) / CLASS B BETA-LACTAMASE


Mass: 24995.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 100 MICROMOLAR ZN IN THE BUFFER / Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: DH1 / Plasmid: PRTWHO12 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 / References: UniProt: P04190, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 38 %
Crystal growpH: 5.6 / Details: SEE IN ACTA CRYSTALLOG PAPER, pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 281 K / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
210 mMcacodylate1drop
30.100 mMdithiothreitol1drop
40.100 mM1dropZnAc2
525 mMcitrate1reservoir
620 %PEG80001reservoir
70.100 mM1reservoirZnAc2
80.100 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.982
DetectorDetector: CCD / Date: Feb 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.982 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 15240 / % possible obs: 80.9 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rsym value: 7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2 % / Rsym value: 10 / % possible all: 79.3
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 77.7 % / Rmerge(I) obs: 0.104

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
XDSdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B.CEREUS EMBO J.

Resolution: 1.85→8 Å / σ(F): 2
Details: FINAL RMS COORD. SHIFT 0.015 ANGSTROMS MEAN B VALUE (MAIN CHAIN, A**2): 13. MEAN B VALUE (SIDE CHAIN, A**2): 15. MEAN B VALUE (SOLVENT, A**2): 26. MEAN B VALUE (ZINC IONS, A**2): 24.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -5 %RANDOM
Rwork0.222 ---
obs0.222 17705 94.1 %-
Refine analyzeLuzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 7 204 1921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg1.7

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