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Yorodumi- PDB-2nxa: Structure of Zn-dependent Metallo-Beta-Lactamase from Bacillus Ce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nxa | ||||||
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Title | Structure of Zn-dependent Metallo-Beta-Lactamase from Bacillus Cereus R121H, C221D Double Mutant | ||||||
Components | Beta-lactamase II | ||||||
Keywords | HYDROLASE / Bacillus cereus / R121H-C221D double mutant | ||||||
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 | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Medrano Martin, F.J. / Vila, A.J. / Gonzalez, J.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The Zn2 position in metallo-beta-lactamases is critical for activity: a study on chimeric metal sites on a conserved protein scaffold. Authors: Gonzalez, J.M. / Medrano Martin, F.J. / Costello, A.L. / Tierney, D.L. / Vila, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nxa.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nxa.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 2nxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nxa_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 2nxa_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 2nxa_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 2nxa_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/2nxa ftp://data.pdbj.org/pub/pdb/validation_reports/nx/2nxa | HTTPS FTP |
-Related structure data
Related structure data | 2nypC 2nzeC 2nzfC 1bc2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24286.621 Da / Num. of mol.: 1 / Mutation: y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: blm / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04190, beta-lactamase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1 M sodium cacodylate, pH 5.4, 60 mM sodium tartrate, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.42 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.42 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 9218 / % possible obs: 94.5 % / Observed criterion σ(I): 29486 / Redundancy: 3.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / % possible all: 70.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BC2 Resolution: 2.29→68.52 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.888 / SU B: 6.983 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.422 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.606 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→68.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.294→2.354 Å / Total num. of bins used: 20
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