+Open data
-Basic information
Entry | Database: PDB / ID: 6rxn | ||||||
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Title | THE STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO DESULFURICANS | ||||||
Components | RUBREDOXIN | ||||||
Keywords | ELECTRON TRANSFER(IRON-SULFUR PROTEIN) | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.5 Å | ||||||
Authors | Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. | ||||||
Citation | Journal: Proteins / Year: 1990 Title: The structure of rubredoxin from Desulfovibrio desulfuricans strain 27774 at 1.5 A resolution. Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. #1: Journal: FEBS Lett. / Year: 1986 Title: Structure of Rubredoxin from the Bacterium Desulfovibrio Desulfuricans Authors: Sieker, L.C. / Stenkamp, R.E. / Jensen, L.H. / Prickril, B. / Legall, J. #2: Journal: J.Mol.Biol. / Year: 1983 Title: Crystallographic Study of Rubredoxin from the Bacterium Desulfovibrio Desulfuricans Strain 27774 Authors: Sieker, L.C. / Jensen, L.H. / Pickril, B.C. / Legall, J. | ||||||
History |
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Remark 700 | SHEET RESIDUES 4 - 7, 11 - 13, AND 48 - 52 DISPLAY A SHEET-LIKE HYDROGEN BONDING PATTERN, BUT THE ...SHEET RESIDUES 4 - 7, 11 - 13, AND 48 - 52 DISPLAY A SHEET-LIKE HYDROGEN BONDING PATTERN, BUT THE TORSION ANGLES FOR THE POLYPEPTIDE CHAIN ARE NOT IDEAL FOR BETA SHEETS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rxn.cif.gz | 20.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rxn.ent.gz | 14.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/6rxn ftp://data.pdbj.org/pub/pdb/validation_reports/rx/6rxn | 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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Atom site foot note | 1: THIS ENTRY CONTAINS ALTERNATE SIDE CHAIN CONFORMATIONS FOR RESIDUES GLU 12, GLN 32, CYS 38, AND LYS 46. 2: RESIDUES 4 - 7, 11 - 13, AND 48 - 52 DISPLAY A SHEET-LIKE HYDROGEN BONDING PATTERN, BUT THE TORSION ANGLES FOR THE POLYPEPTIDE CHAIN ARE NOT IDEAL FOR BETA SHEETS. |
-Components
#1: Protein/peptide | Mass: 5129.667 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / References: UniProt: P04170 |
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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: 1.62 Å3/Da / Density % sol: 23.87 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 23 ℃ / 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: 1.5 Å / Num. measured all: 11616 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.5→5 Å Details: THE FE ATOM HAS BEEN REFINED WITH AN ANISOTROPIC TEMPERATURE FACTOR. THE VALUE GIVEN IN THE B-VALUE FIELD IS THE EQUIVALENT B-VALUE. (B(EQ) = 8*PI**2*(U11+U22+U33)/3). THE ANISOTROPIC ...Details: THE FE ATOM HAS BEEN REFINED WITH AN ANISOTROPIC TEMPERATURE FACTOR. THE VALUE GIVEN IN THE B-VALUE FIELD IS THE EQUIVALENT B-VALUE. (B(EQ) = 8*PI**2*(U11+U22+U33)/3). THE ANISOTROPIC TEMPERATURE FACTORS FOR THE FE IN U(IJ) ARE U(1,1) = 0.0923 U(2,2) = 0.0932 U(3,3) = 0.0762 U(1,2) = 0.0132 U(1,3) = -0.0013 U(2,3) = -0.0030
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Refinement step | Cycle: LAST / Resolution: 1.5→5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 5 Å / Num. reflection obs: 4867 / Rfactor obs: 0.093 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |