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Yorodumi- PDB-5cxk: Crystal structure of beta carbonic anhydrase from Vibrio cholerae -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cxk | ||||||
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Title | Crystal structure of beta carbonic anhydrase from Vibrio cholerae | ||||||
Components | Carbonic anhydrase | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Ferraroni, M. / Supuran, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Crystal structure and kinetic studies of a tetrameric type II beta-carbonic anhydrase from the pathogenic bacterium Vibrio cholerae. Authors: Ferraroni, M. / Del Prete, S. / Vullo, D. / Capasso, C. / Supuran, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cxk.cif.gz | 365.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cxk.ent.gz | 298.6 KB | Display | PDB format |
PDBx/mmJSON format | 5cxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/5cxk ftp://data.pdbj.org/pub/pdb/validation_reports/cx/5cxk | HTTPS FTP |
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-Related structure data
Related structure data | 2esfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25198.596 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: can, DN30_1616 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A086SLX8, carbonic anhydrase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-BCT / #4: 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: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG8000, ethylene glycol,Hepes |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→47.5 Å / Num. obs: 166608 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 28.602 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.092 / Χ2: 0.954 / Net I/σ(I): 10.82 / Num. measured all: 501239 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.527
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ESF Resolution: 1.9→47.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.1818 / FOM work R set: 0.8466 / SU B: 2.157 / SU ML: 0.07 / SU R Cruickshank DPI: 0.0295 / SU Rfree: 0.0302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 56.55 Å2 / Biso mean: 22.753 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 1.9→47.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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