+Open data
-Basic information
Entry | Database: PDB / ID: 2cvw | ||||||
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Title | Structures of Yeast Ribonucleotide Reductase I | ||||||
Components | Ribonucleoside-diphosphate reductase large chain 1 | ||||||
Keywords | OXIDOREDUCTASE / Eukaryotic / Ribonucleotide Reductase / dNTP Regulation | ||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / nucleotide binding / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Xu, H. / Faber, C. / Uchiki, T. / Fairman, J.W. / Racca, J. / Dealwis, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation Authors: Xu, H. / Faber, C. / Uchiki, T. / Fairman, J.W. / Racca, J. / Dealwis, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cvw.cif.gz | 151 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cvw.ent.gz | 114.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/2cvw ftp://data.pdbj.org/pub/pdb/validation_reports/cv/2cvw | HTTPS FTP |
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-Related structure data
Related structure data | 1zyzC 1zzdC 2cvsC 2cvtC 2cvuC 2cvvC 2cvxC 2cvyC 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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Unit cell |
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Details | The second part of the active biological dimer assembly is generated by the two fold axis: -x, -y+1, z. |
-Components
#1: Protein | Mass: 99672.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pWJ751-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P21524, ribonucleoside-diphosphate reductase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-TTP / |
#4: Chemical | ChemComp-GDP / |
#5: 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: 2.04 Å3/Da / Density % sol: 37.3 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6.5 Details: PEG 3350, sodium acetate, ammonium sulfate, pH 6.5, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 32305 / Num. obs: 32305 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3193 / Rsym value: 0.42 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: native structure Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.856 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.432 / ESU R Free: 0.286 / 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: 43.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.399→2.461 Å / Total num. of bins used: 20
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