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Yorodumi- PDB-1h0o: Cobalt substitution of mouse R2 ribonucleotide reductase to model... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h0o | ||||||
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Title | Cobalt substitution of mouse R2 ribonucleotide reductase to model the reactive diferrous state | ||||||
Components | RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / RIBONUCLEOTIDE REDUCTASE / DINUCLEAR METAL-CLUSTER | ||||||
Function / homology | Function and homology information deoxyribonucleotide metabolic process / Interconversion of nucleotide di- and triphosphates / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein heterotetramerization / positive regulation of G1/S transition of mitotic cell cycle ...deoxyribonucleotide metabolic process / Interconversion of nucleotide di- and triphosphates / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein heterotetramerization / positive regulation of G1/S transition of mitotic cell cycle / blastocyst development / ferric iron binding / nuclear envelope / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Strand, K.R. / Karlsen, S. / Andersson, K.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Cobalt Substitution of Mouse R2 Ribonucleotide Reductase as a Model for Thereactive Diferrous State. Spectroscopic and Structural Evidence for a Ferromagnetically Coupled Dinuclear Cobalt Cluster Authors: Strand, K.R. / Karlsen, S. / Andersson, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h0o.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h0o.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h0o_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 1h0o_full_validation.pdf.gz | 431 KB | Display | |
Data in XML | 1h0o_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 1h0o_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/1h0o ftp://data.pdbj.org/pub/pdb/validation_reports/h0/1h0o | HTTPS FTP |
-Related structure data
Related structure data | 1h0nC 1xsmS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 45149.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COBALT-SUBSTITUTED / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P11157, ribonucleoside-diphosphate reductase |
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#2: Chemical | ChemComp-CO / |
#3: Water | ChemComp-HOH / |
Compound details | DNA SYNTHESIS PRECURSOR PROVIDER |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.05 % | ||||||||||||||||||||||||||||
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Crystal grow | pH: 4.7 Details: 0.1 M NA-ACETATE BUFFER PH4.7, 1.2 M NACL, 7.5 MG/ML APO-R2 PROTEIN. CRYSTALS WERE MADE BY CO-CRYSTALLISATION (3.8 EQV. CO2+)., pH 4.70 | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: MARRESEARCH / Detector: CCD / Date: Mar 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 22045 / Biso Wilson estimate: 25.1 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XSM Resolution: 2.2→8 Å / Data cutoff high absF: 572486.45 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.3783 Å2 / ksol: 0.384623 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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