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- PDB-2bmi: METALLO-BETA-LACTAMASE -

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Basic information

Entry
Database: PDB / ID: 2bmi
TitleMETALLO-BETA-LACTAMASE
ComponentsPROTEIN (CLASS B BETA-LACTAMASE)
KeywordsHYDROLASE / 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 / : / 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 speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCarfi, A. / Duee, E. / Dideberg, O.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: X-ray structure of the ZnII beta-lactamase from Bacteroides fragilis in an orthorhombic crystal form.
Authors: Carfi, A. / Duee, E. / Paul-Soto, R. / 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 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 23, 1998Provider: repository / Type: Initial release
SupersessionApr 12, 2000ID: 1BMI
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,0258
Polymers50,7172
Non-polymers3086
Water7,548419
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.256, 94.920, 111.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25358.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: METALLO-BETA-LACTAMASE, CLASS B BETA-LACTAMASE / Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: BL21 / Gene: CCRA / Plasmid: PJST241 / Species (production host): Escherichia coli / Gene (production host): CCRA / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25910, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.6 Å3/Da / Density % sol: 45 %
Crystal growpH: 9
Details: FORM II CRYSTAL IN ACTA CRYST(1997) D53 485-487, pH 9.0
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
Temperature: 288 K / Method: vapor diffusion, hanging drop / Details: Carfi, A., (1997) Acta Crystallogr., D53, 485. / PH range low: 9 / PH range high: 8.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.0 mg/mlprotein1drop
222-24 %(w/v)PEG80001reservoir
30.100 mMdithiothreitol1reservoir
4100 mMBicine1reservoir
50.2-1 mM1reservoirZnAc2
62-5 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 7, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→28 Å / Num. obs: 32806 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rsym value: 7
Reflection shellResolution: 2→2.12 Å / Rsym value: 16 / % possible all: 91.8
Reflection
*PLUS
% possible obs: 94.9 % / Num. measured all: 191117 / Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
AMoRE(NAVAZA)phasing
CCP4model building
X-PLOR3.1refinement
XDSdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / σ(F): 0
Details: FINAL RMS COORDINATE SHIFT 0.015 ANGSTROMS, MEAN B VALUE (MAIN CHAIN, A**2): 15, MEAN B VALUE (SIDE CHAIN, A**2): 17, MEAN B VALUE (SOLVENT, A**2): 33, MEAN B VALUE (ZINC IONS, A**2): 13
RfactorNum. reflection% reflectionSelection details
Rfree0.262 -5 %RANDOM
Rwork0.196 ---
obs0.196 32501 94.6 %-
Refine analyzeLuzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 6 438 3955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.6
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: 10 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.6

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