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Yorodumi- PDB-3kzv: The crystal structure of a cytoplasmic protein with unknown funct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kzv | ||||||
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Title | The crystal structure of a cytoplasmic protein with unknown function from Saccharomyces cerevisiae | ||||||
Components | Uncharacterized oxidoreductase YIR035C | ||||||
Keywords | OXIDOREDUCTASE / cytoplasmic protein / unknown function / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / Oxidoreductases / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Zhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a cytoplasmic protein with unknown function from Saccharomyces cerevisiae Authors: Zhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kzv.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kzv.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 3kzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kzv_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 3kzv_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 3kzv_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3kzv_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/3kzv ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kzv | 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 on special symmetry positions |
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Details | This protein exists as tetramer. The other parts of the biological assembly is generated by the operations: -y+1/2,-x+1/2,-z+1/2 y+1/2,x-1/2,-z+1/2 x+1,-y,z |
-Components
#1: Protein | Mass: 27508.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288C / Gene: GI:6322226, YIR035C / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P40579, Oxidoreductases | ||
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#2: Chemical | #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: 2.8 Å3/Da / Density % sol: 56.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M Bis-tris, 5% Iso-propanol, 2.4M NH4SO4,1/1600 chymotrypsin, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2→83.05 Å / Num. all: 20314 / Num. obs: 20048 / % possible obs: 98.69 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 16.3 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 1.5 |
Reflection shell | Resolution: 2→2.052 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 36.9 / Num. unique all: 1558 / % possible all: 93.58 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→83.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.978 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.16 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.676 Å2
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Refinement step | Cycle: LAST / Resolution: 2→83.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 42.648 Å / Origin y: 5.353 Å / Origin z: 7.607 Å
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Refinement TLS group |
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