[English] 日本語
Yorodumi- PDB-1sms: Structure of the Ribonucleotide Reductase Rnr4 Homodimer from Sac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sms | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the Ribonucleotide Reductase Rnr4 Homodimer from Saccharomyces cerevisiae | ||||||
Components | Ribonucleoside-diphosphate reductase small chain 2 | ||||||
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 / protein heterodimerization activity / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1sms.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1sms.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 1sms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sms_validation.pdf.gz | 380.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1sms_full_validation.pdf.gz | 424.7 KB | Display | |
Data in XML | 1sms_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1sms_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/1sms ftp://data.pdbj.org/pub/pdb/validation_reports/sm/1sms | HTTPS FTP |
-Related structure data
Related structure data | 1smqC 1jk0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40102.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RNR4, YGR180C / Production host: Escherichia coli (E. coli) References: UniProt: P49723, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-HG / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.53 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, PEG 1000, Ethanol, sodium chloride, EMTS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
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→12 Å / Num. obs: 239131 / % possible obs: 93.6 % / Rsym value: 0.088 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 3.1→3.15 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.424 / % possible all: 94.1 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JK0 subunit Y4 Resolution: 3.1→12 Å / Cross valid method: THROUGHOUT
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→12 Å
| ||||||||||||||||
Refine LS restraints |
|