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Yorodumi- PDB-3qwa: Crystal structure of Saccharomyces cerevisiae Zeta-crystallin-lik... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qwa | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae Zeta-crystallin-like quinone oxidoreductase Zta1 | ||||||
Components | Probable quinone oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / quinone oxidoreductases / NADPH binding / cytoplasm and nucleus | ||||||
Function / homology | Function and homology information NADPH:quinone reductase / 2-alkenal reductase [NAD(P)+] activity / NADPH:quinone reductase activity / mRNA 3'-UTR AU-rich region binding / NADPH binding / cellular response to oxidative stress / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Guo, P.C. / Ma, X.X. / Bao, Z.Z. / Chen, Y.X. / Zhou, C.Z. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Structural insights into the cofactor-assisted substrate recognition of yeast quinone oxidoreductase Zta1 Authors: Guo, P.C. / Ma, X.X. / Bao, Z.Z. / Ma, J.D. / Chen, Y. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qwa.cif.gz | 281 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qwa.ent.gz | 229 KB | Display | PDB format |
PDBx/mmJSON format | 3qwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qwa_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 3qwa_full_validation.pdf.gz | 431.4 KB | Display | |
Data in XML | 3qwa_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 3qwa_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/3qwa ftp://data.pdbj.org/pub/pdb/validation_reports/qw/3qwa | HTTPS FTP |
-Related structure data
Related structure data | 3qwbC 1qorS C: citing same article (ref.) S: Starting model for refinement |
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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: 37063.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288C / Gene: YBR0421, YBR046C, ZTA1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38230, NADPH:quinone reductase #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: 2.22 Å3/Da / Density % sol: 44.57 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% polyethylene glycol 3350, 0.2M MgCl2, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 45227 / Num. obs: 45227 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 22.89 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 7.73 / Num. unique all: 4464 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QOR Resolution: 2→35.32 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.102 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R Free: 0.187 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.604 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.32 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 / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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