+Open data
-Basic information
Entry | Database: PDB / ID: 2uw2 | |||||||||
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Title | Crystal structure of human ribonucleotide reductase subunit R2 | |||||||||
Components | RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 SUBUNIT | |||||||||
Keywords | OXIDOREDUCTASE / SMALL SUBUNIT RIBONUCLEOTIDE REDUCTASE / R2 / IRON / DIIRON / RADICAL / R2 SUBUNIT / METAL-BINDING / RIBONUCLEOTIDE REDUCTASE / DNA REPLICATION / PHOSPHORYLATION | |||||||||
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: 2.8 Å | |||||||||
Authors | Welin, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. ...Welin, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Kotenyova, T. / Magnusdottir, A. / Moche, M. / Nilsson-Ehle, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Stenmark, P. / Uppenberg, J. / Thorsell, A.G. / Van Den Berg, S. / Wallden, K. / Weigelt, J. / Nordlund, P. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Ribonucleotide Reductase Subunit R2 Authors: Welin, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg ...Authors: Welin, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Kotenyova, T. / Magnusdottir, A. / Moche, M. / Nilsson-Ehle, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Stenmark, P. / Uppenberg, J. / Thorsell, A.G. / Van Den Berg, S. / Wallden, K. / Weigelt, J. / Nordlund, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uw2.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uw2.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 2uw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/2uw2 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/2uw2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38693.270 Da / Num. of mol.: 1 / Fragment: RESIDUES 60-389 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P31350, ribonucleoside-diphosphate reductase |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
Sequence details | THE PRESENT SEQUENCE CARRIES A PRO AT POSITION 251. THIS DIFFERS FROM THE UNIPROT SEQUENCE, WHICH ...THE PRESENT SEQUENCE CARRIES A PRO AT POSITION 251. THIS DIFFERS FROM THE UNIPROT SEQUENCE, WHICH CARRIES A LEU AT POSITION 251. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.28 % |
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Crystal grow | pH: 5.5 / Details: 0.1M BISTRIS PH 5.5, 0.12M AMAC, 11% PEG 10K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 21, 2006 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 10697 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.05 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.12 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.865 / SU B: 16.326 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.12 Å
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