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Open data
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Basic information
Entry | Database: PDB / ID: 2cvu | ||||||
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Title | Structures of Yeast Ribonucleotide Reductase I | ||||||
![]() | Ribonucleoside-diphosphate reductase large chain 1 | ||||||
![]() | OXIDOREDUCTASE / Eukaryotic / Ribonucleotide Reductase / dNTP Regulation | ||||||
Function / homology | ![]() Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / nucleotide binding / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, H. / Faber, C. / Uchiki, T. / Fairman, J.W. / Racca, J. / Dealwis, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.9 KB | Display | ![]() |
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PDB format | ![]() | 114.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1zyzC ![]() 1zzdC ![]() 2cvsC ![]() 2cvtC ![]() 2cvvC ![]() 2cvwC ![]() 2cvxC ![]() 2cvyC C: citing same article ( |
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Similar structure data |
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Links
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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. |
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Components
#1: Protein | Mass: 99672.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pWJ751-3 / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: P21524, ribonucleoside-diphosphate reductase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-CDP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 29, 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: 2.9→50 Å / Num. all: 18752 / Num. obs: 18752 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2553 / Rsym value: 0.408 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: native structure Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.897 / SU B: 14.113 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / 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: 37.403 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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