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Yorodumi- PDB-3tb9: Structure of Yeast Ribonucleotide Reductase 1 Q288A with AMPPNP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tb9 | ||||||
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Title | Structure of Yeast Ribonucleotide Reductase 1 Q288A with AMPPNP and CDP | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.53 Å | ||||||
Authors | Ahmad, M.F. / Kaushal, P.S. / Wan, Q. / Wijeratna, S.R. / Huang, M. / Dealwis, C.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Role of Arginine 293 and Glutamine 288 in Communication between Catalytic and Allosteric Sites in Yeast Ribonucleotide Reductase. Authors: Ahmad, M.F. / Kaushal, P.S. / Wan, Q. / Wijerathna, S.R. / An, X. / Huang, M. / Dealwis, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tb9.cif.gz | 148.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tb9.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 3tb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/3tb9 ftp://data.pdbj.org/pub/pdb/validation_reports/tb/3tb9 | HTTPS FTP |
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-Related structure data
Related structure data | 3tbaC 2cvuS 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
#1: Protein | Mass: 99615.930 Da / Num. of mol.: 1 / Mutation: Q288A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RNR1, CRT7, RIR1, 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-CDP / |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-MG / |
#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: 39.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES pH 7.0, 15-25% PEG 3350, 0.2M NaCl, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2011 |
Radiation | Monochromator: Single-crystal side bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→50 Å / Num. all: 28484 / Num. obs: 28484 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rsym value: 0.105 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.53→2.59 Å / Redundancy: 8 % / Mean I/σ(I) obs: 5 / Rsym value: 0.519 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2CVU Resolution: 2.53→43.48 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / ESU R: 0.601 / 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: 39.857 Å2
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Refinement step | Cycle: LAST / Resolution: 2.53→43.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.53→2.596 Å / Total num. of bins used: 20
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