+Open data
-Basic information
Entry | Database: PDB / ID: 1zzd | ||||||
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Title | Structures of Yeast Ribonucleotide Reductase I | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Eukaryotic / Ribonucleotide Reductase / dNTP Regulation | ||||||
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 / protein heterodimerization activity / 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: 2.6 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 | 1zzd.cif.gz | 144.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zzd.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zzd_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 1zzd_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 1zzd_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 1zzd_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/1zzd ftp://data.pdbj.org/pub/pdb/validation_reports/zz/1zzd | HTTPS FTP |
-Related structure data
Related structure data | 1zyzC 2cvsC 2cvtC 2cvuC 2cvvC 2cvwC 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) Gene: RNR1 / 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: Protein/peptide | Mass: 1143.180 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chemically synthesized, this sequene occurs naturally in yeast. References: UniProt: P49723, ribonucleoside-diphosphate reductase |
#3: 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 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 22, 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: 2.6→50 Å / Num. all: 26145 / Num. obs: 26145 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2587 / Rsym value: 0.736 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: native structure Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.671 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.788 / ESU R Free: 0.331 / 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: 46.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.663 Å / Total num. of bins used: 20
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