+Open data
-Basic information
Entry | Database: PDB / ID: 3s87 | ||||||
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Title | Structure of Yeast Ribonucleotide Reductase 1 with dGTP and ADP | ||||||
Components | Ribonucleoside-diphosphate reductase large chain 1 | ||||||
Keywords | OXIDOREDUCTASE / dNTP regulation / allostery | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Isomorphous / Resolution: 2.25 Å | ||||||
Authors | Ahmad, M.F. / Kaushal, P.S. / Wan, Q. / Wijeratna, S.R. / Huang, M. / Dealwis, C.D. | ||||||
Citation | Journal: To be Published Title: Structural and biochemical basis of lethal mutant R293A of yeast ribonucleotide reductase Authors: Ahmad, M.F. / Kaushal, P.S. / Wan, Q. / Wijeratna, S.R. / Huang, M. / Dealwis, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s87.cif.gz | 155.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s87.ent.gz | 117.2 KB | Display | PDB format |
PDBx/mmJSON format | 3s87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s87_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3s87_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3s87_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 3s87_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/3s87 ftp://data.pdbj.org/pub/pdb/validation_reports/s8/3s87 | HTTPS FTP |
-Related structure data
Related structure data | 3s8aC 3s8bC 3s8cC 2cvxS S: Starting model for refinement 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 99672.984 Da / Num. of mol.: 1 / Fragment: Ribonucleotide Reductase 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: CRT7, RIR1, RNR1, Saccharomyces, SDS12, YER070W / Plasmid: pWJ751-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P21524, ribonucleoside-diphosphate reductase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-DGT / |
#4: Chemical | ChemComp-ADP / |
#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: 2.07 Å3/Da / Density % sol: 40.66 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 Details: 20-25% PEG 3350, 0.1 M HEPES, 0.1 M sodium chloride, pH 7.0, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 2, 2010 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. obs: 35900 / % possible obs: 99.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.07 / Num. unique all: 2950 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: Isomorphous Starting model: 2CVX Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.531 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 45.436 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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