+
Open data
-
Basic information
Entry | Database: PDB / ID: 2cvy | ||||||
---|---|---|---|---|---|---|---|
Title | Structures of Yeast Ribonucleotide Reductase I | ||||||
![]() |
| ||||||
![]() | 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 / ferrous iron binding / molecular adaptor activity / protein heterodimerization activity / nucleotide binding / zinc ion binding ...Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / ferrous iron binding / molecular adaptor activity / protein heterodimerization activity / nucleotide binding / zinc ion 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 148.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 112.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1zyzC ![]() 1zzdC ![]() 2cvsC ![]() 2cvtC ![]() 2cvuC ![]() 2cvvC ![]() 2cvwC ![]() 2cvxC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
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.) ![]() ![]() Plasmid: pWJ751-3 / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: P21524, ribonucleoside-diphosphate reductase |
---|---|
#2: Protein/peptide | Mass: 1047.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesized References: UniProt: P09938, ribonucleoside-diphosphate reductase |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-TTP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 37.3 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 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: 32238 / Num. obs: 32238 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3131 / Rsym value: 0.472 / % possible all: 97 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: native structure Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.851 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 47.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.396→2.458 Å / Total num. of bins used: 20
|