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Yorodumi- PDB-2nze: Structure of beta-lactamase II from Bacillus cereus. R121H, C221S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nze | ||||||
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Title | Structure of beta-lactamase II from Bacillus cereus. R121H, C221S double mutant. Space group P3121. | ||||||
Components | Beta-lactamase II | ||||||
Keywords | HYDROLASE / Beta-Lactamase II / Bacillus cereus | ||||||
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: 1.8 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 | 2nze.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nze.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 2nze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nze_validation.pdf.gz | 471.5 KB | Display | wwPDB validaton report |
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Full document | 2nze_full_validation.pdf.gz | 475.4 KB | Display | |
Data in XML | 2nze_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 2nze_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/2nze ftp://data.pdbj.org/pub/pdb/validation_reports/nz/2nze | HTTPS FTP |
-Related structure data
Related structure data | 2nxaC 2nypC 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 24387.791 Da / Num. of mol.: 2 / Mutation: yes 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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-Non-polymers , 5 types, 384 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ACY / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 0.1 M sodium acetate, 2.8 M ammonium sulfate, pH 4.9, 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: 1.8→50 Å / Num. obs: 40696 / % possible obs: 94.8 % / Observed criterion σ(I): 202606 / Redundancy: 5.2 % / Rsym value: 0.061 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.45 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1bc2 Resolution: 1.8→58.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.457 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.127 / 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: 23.194 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→58.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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