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Yorodumi- PDB-3olj: Crystal structure of human ribonucleotide reductase subunit M2 (hRRM2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3olj | ||||||
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Title | Crystal structure of human ribonucleotide reductase subunit M2 (hRRM2) | ||||||
Components | Ribonucleoside-diphosphate reductase subunit M2Ribonucleotide reductase | ||||||
Keywords | OXIDOREDUCTASE / Metal-binding / hRRM2 | ||||||
Function / homology | Function and homology information ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / Interconversion of nucleotide di- and triphosphates / deoxyribonucleotide biosynthetic process / protein heterotetramerization / G1/S-Specific Transcription / Transcriptional Regulation by E2F6 ...ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / Interconversion of nucleotide di- and triphosphates / deoxyribonucleotide biosynthetic process / protein heterotetramerization / G1/S-Specific Transcription / Transcriptional Regulation by E2F6 / blastocyst development / positive regulation of G1/S transition of mitotic cell cycle / ferric iron binding / protein homodimerization activity / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Chen, X.H. / Xu, Z.J. / Chen, B.E. / Jiang, H.J. / Yang, C.G. / Zhu, W.L. / Shao, J.M. | ||||||
Citation | Journal: To be Published Title: hRRM2 Authors: Chen, X.H. / Xu, Z.J. / Chen, B.E. / Jiang, H.J. / Yang, C.G. / Zhu, W.L. / Shao, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3olj.cif.gz | 252.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3olj.ent.gz | 203.5 KB | Display | PDB format |
PDBx/mmJSON format | 3olj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/3olj ftp://data.pdbj.org/pub/pdb/validation_reports/ol/3olj | HTTPS FTP |
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-Related structure data
Related structure data | 1w69S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33619.734 Da / Num. of mol.: 4 / Fragment: UNP residues 66-350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RRM2, RR2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P31350, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.4M NaH2PO4/K2HPO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 123466 / Num. obs: 118751 / % possible obs: 96.181 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.4 / Redundancy: 7.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.36 / Num. unique all: 9570 / Rsym value: 0.653 / % possible all: 78.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W69 Resolution: 2.1→39.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.221 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(I): 1.36 / ESU R Free: 0.154 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.929 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→39.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.098→2.152 Å / Total num. of bins used: 20
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