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Open data
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Basic information
Entry | Database: PDB / ID: 2bmi | |||||||||
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Title | METALLO-BETA-LACTAMASE | |||||||||
![]() | PROTEIN (CLASS B BETA-LACTAMASE) | |||||||||
![]() | HYDROLASE / BETA-LACTAMASE / METALLO BETA-LACTAMASE / ZINC | |||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Carfi, A. / Duee, E. / Dideberg, O. | |||||||||
![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.4 KB | Display | ![]() |
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PDB format | ![]() | 82.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 365.7 KB | Display | ![]() |
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Full document | ![]() | 368.1 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | 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.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 7, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→28 Å / Num. obs: 32806 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rsym value: 7 |
Reflection shell | Resolution: 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
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Refinement | Method to determine structure: ![]() 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
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Refine analyze | Luzzati sigma a obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |