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Yorodumi- PDB-1smq: Structure of the Ribonucleotide Reductase Rnr2 Homodimer from Sac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1smq | ||||||
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Title | Structure of the Ribonucleotide Reductase Rnr2 Homodimer from Saccharomyces cerevisiae | ||||||
Components | Ribonucleoside-diphosphate reductase small chain 1 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 / ferrous iron binding / molecular adaptor activity / protein heterodimerization activity / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Sommerhalter, M. / Voegtli, W.C. / Perlstein, D.L. / Ge, J. / Stubbe, J. / Rosenzweig, A.C. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structures of the yeast ribonucleotide reductase Rnr2 and Rnr4 homodimers. Authors: Sommerhalter, M. / Voegtli, W.C. / Perlstein, D.L. / Ge, J. / Stubbe, J. / Rosenzweig, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1smq.cif.gz | 244.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1smq.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 1smq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1smq_validation.pdf.gz | 397.6 KB | Display | wwPDB validaton report |
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Full document | 1smq_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 1smq_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 1smq_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/1smq ftp://data.pdbj.org/pub/pdb/validation_reports/sm/1smq | HTTPS FTP |
-Related structure data
Related structure data | 1smsC 1jk0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46207.297 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RNR2, YJL026W, J1271 / Production host: Escherichia coli (E. coli) References: UniProt: P09938, ribonucleoside-diphosphate reductase |
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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: 2.82 Å3/Da / Density % sol: 56.43 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: Succinate, PEG3350, lithium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→87 Å / Num. obs: 168766 / % possible obs: 94.6 % / Rsym value: 0.059 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 3.1→3.27 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.294 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JK0 subunit Y2 Resolution: 3.1→25 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 3.1→25 Å
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Refine LS restraints |
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