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Yorodumi- PDB-3f13: Crystal structure of putative nudix hydrolase family member from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f13 | ||||||
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Title | Crystal structure of putative nudix hydrolase family member from Chromobacterium violaceum | ||||||
Components | putative nudix hydrolase family member | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chromobacterium violaceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Bonanno, J.B. / Freeman, J. / Bain, K.T. / Do, J. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative nudix hydrolase family member from Chromobacterium violaceum Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Do, J. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f13.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f13.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 3f13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f13_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 3f13_full_validation.pdf.gz | 445.7 KB | Display | |
Data in XML | 3f13_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 3f13_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/3f13 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/3f13 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18517.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CV_1928 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7NWQ3 #2: 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: 2.28 Å3/Da / Density % sol: 46.03 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7 Details: 19% PEG 3350, 600mM ammonium chloride, pH 7.0, Vapor diffusion, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 26, 2008 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→52.882 Å / Num. all: 35983 / Num. obs: 34975 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2 / Num. measured all: 19331 / Num. unique all: 5017 / Rsym value: 0.511 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 1.806 / WRfactor Rwork: 0.426 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.771 / SU B: 3.011 / SU ML: 0.098 / SU R Cruickshank DPI: 0.124 / SU Rfree: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.124 / ESU R Free: 0.125 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.36 Å2 / Biso mean: 35.158 Å2 / Biso min: 16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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