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Yorodumi- PDB-1rdg: RUBREDOXIN FROM DESULFOVIBRIO GIGAS. A MOLECULAR MODEL OF THE OXI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rdg | ||||||
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Title | RUBREDOXIN FROM DESULFOVIBRIO GIGAS. A MOLECULAR MODEL OF THE OXIDIZED FORM AT 1.4 ANGSTROMS RESOLUTION | ||||||
Components | RUBREDOXIN | ||||||
Keywords | ELECTRON TRANSFER(IRON-SULFUR PROTEIN) | ||||||
Function / homology | Function and homology information alkane catabolic process / electron transfer activity / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Desulfovibrio gigas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | ||||||
Authors | Frey, M. / Sieker, L.C. / Payan, F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1987 Title: Rubredoxin from Desulfovibrio gigas. A molecular model of the oxidized form at 1.4 A resolution. Authors: Frey, M. / Sieker, L. / Payan, F. / Haser, R. / Bruschi, M. / Pepe, G. / LeGall, J. #1: Journal: J.Mol.Biol. / Year: 1976 Title: Some Comparisons between Two Crystallized Anaerobic Bacterial Rubredoxins from Desulfovibrio Gigas and D. Vulgaris Authors: Pierrot, M. / Haser, R. / Frey, M. / Bruschi, M. / Legall, J. / Sieker, L.C. / Jensen, L.H. #2: Journal: Biochem.Biophys.Res.Commun. / Year: 1976 Title: The Amino Acid Sequence of Rubredoxin from the Sulfate Reducing Bacterium, Desulfovibrio Gigas Authors: Bruschi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rdg.cif.gz | 24.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rdg.ent.gz | 14.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rdg_validation.pdf.gz | 408 KB | Display | wwPDB validaton report |
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Full document | 1rdg_full_validation.pdf.gz | 408.3 KB | Display | |
Data in XML | 1rdg_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1rdg_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/1rdg ftp://data.pdbj.org/pub/pdb/validation_reports/rd/1rdg | HTTPS FTP |
-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: 5682.304 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio gigas (bacteria) / References: UniProt: P00270 | ||
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#2: Chemical | ChemComp-FE / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.66 Å3/Da / Density % sol: 26.11 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 27 ℃ / pH: 4 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 2 Å / Num. obs: 7355 / Num. measured all: 10531 / Biso Wilson estimate: 9.1 Å2 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.136 / Highest resolution: 1.4 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.4 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 7090 / σ(F): 2 / Highest resolution: 1.4 Å / Rfactor obs: 0.136 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |