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Yorodumi- PDB-4rxn: CRYSTALLOGRAPHIC REFINEMENT OF RUBREDOXIN AT 1.2 ANGSTROMS RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rxn | |||||||||
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Title | CRYSTALLOGRAPHIC REFINEMENT OF RUBREDOXIN AT 1.2 ANGSTROMS RESOLUTION | |||||||||
Components | RUBREDOXIN | |||||||||
Keywords | ELECTRON TRANSFER(IRON-SULFUR PROTEIN) | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium pasteurianum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.2 Å | |||||||||
Authors | Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1980 Title: Crystallographic refinement of rubredoxin at 1 x 2 A degrees resolution. Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. #1: Journal: J.Mol.Biol. / Year: 1979 Title: The Structure of Rubredoxin at 1.2 Angstroms Resolution Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. #2: Journal: J.Mol.Biol. / Year: 1978 Title: Water Structure in a Protein Crystal. Rubredoxin at 1.2 Angstroms Resolution. Authors: Watenpaugh, K.D. / Margulis, T.N. / Sieker, L.C. / Jensen, L.H. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1973 Title: Refinement of the Model of a Protein. Rubredoxin at 1.5 Angstroms Resolution Authors: Watenpaugh, K.D. / Sieker, L.C. / Herriott, J.R. / Jensen, L.H. #4: Journal: J.Mol.Biol. / Year: 1973 Title: Sequence of Rubredoxin by X-Ray Diffraction Authors: Herriott, J.R. / Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. #5: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972 Title: The Structure of a Non-Heme Iron Protein, Rubredoxin at 1.5 Angstroms Resolution Authors: Watenpaugh, K.D. / Sieker, L.C. / Herriott, J.R. / Jensen, L.H. #6: Journal: Thesis / Year: 1972 Title: The Primary Structure of Clostridium Pasteurianum Rubredoxin Authors: Mccarthy, K.F. #7: Journal: J.Mol.Biol. / Year: 1970 Title: Structure of Rubredoxin. An X-Ray Study to 2.5 Angstroms Resolution Authors: Herriott, J.R. / Sieker, L.C. / Jensen, L.H. / Lovenberg, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rxn.cif.gz | 34.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rxn.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 4rxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/4rxn ftp://data.pdbj.org/pub/pdb/validation_reports/rx/4rxn | 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: 6054.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium pasteurianum (bacteria) / References: UniProt: P00268 |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow | *PLUS Temperature: 23 ℃ / pH: 4 / Method: unknown / Details: salting out |
Components of the solutions | *PLUS Conc.: 80 %sat / Chemical formula: (NH4)2SO4 |
-Data collection
Reflection | *PLUS Observed criterion σ(I): 4 / Num. measured all: 17000 / Rmerge(I) obs: 0.038 |
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-Processing
Refinement | Resolution: 1.2→10 Å Details: EACH HYDROGEN ATOM POSITION HAS BEEN CALCULATED FROM THE COORDINATES OF THE ATOM IT IS BONDED TO. THE B-VALUE OF THE HEAVIER ATOM WAS ASSIGNED TO THE HYDROGEN ATOM. THE CELL DIMENSIONS ...Details: EACH HYDROGEN ATOM POSITION HAS BEEN CALCULATED FROM THE COORDINATES OF THE ATOM IT IS BONDED TO. THE B-VALUE OF THE HEAVIER ATOM WAS ASSIGNED TO THE HYDROGEN ATOM. THE CELL DIMENSIONS VARIED FROM START TO FINISH OF DATA COLLECTION. THE VALUES GIVEN ARE THOSE AT THE MID-POINT OF DATA COLLECTION.
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Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refinement | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 10 Å / Num. reflection obs: 10936 / σ(I): 2 / Rfactor obs: 0.128 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS Biso mean: 12 Å2 |