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Yorodumi- PDB-1rdv: RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, TRIGONAL CRYST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rdv | ||||||
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Title | RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, TRIGONAL CRYSTAL FORM | ||||||
Components | RUBREDOXIN | ||||||
Keywords | ELECTRON TRANSFER / RUBREDOXIN / METALLOPROTEIN / SULFATE-REDUCING BACTERIUM / 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 vulgaris str. 'Miyazaki F' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Higuchi, Y. / Yasuoka, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms. Authors: Misaki, S. / Morimoto, Y. / Ogata, M. / Yagi, T. / Higuchi, Y. / Yasuoka, N. #1: Journal: Protein Pept.Lett. / Year: 1998 Title: Preliminary Crystallographic Study of Two Crystal Forms of Rubredoxin from Sulfate-Reducing Bacterium Authors: Higuchi, Y. / Sugiyama, M.S. / Morimoto, S. / Ogata, Y. / Yagi, M. / Yasuoka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rdv.cif.gz | 21 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rdv.ent.gz | 12.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/1rdv ftp://data.pdbj.org/pub/pdb/validation_reports/rd/1rdv | HTTPS FTP |
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-Related structure data
Related structure data | 2rdvC 7rxnS 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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Unit cell |
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-Components
#1: Protein | Mass: 5602.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: IAM 12604 Source: (natural) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) Species: Desulfovibrio vulgaris / Strain: MIYAZAKI F / References: UniProt: P15412 |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / pH: 7 / Method: microdialysis / Details: Higuchi, Y., (1998) Protein Pept.Lett., 5, 175. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 10630 / % possible obs: 53.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.089 |
Reflection | *PLUS Num. obs: 2541 / Observed criterion σ(I): 3 / Num. measured all: 10630 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 7RXN Resolution: 2→20 Å / Isotropic thermal model: RESTRAINED / σ(F): 3
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Displacement parameters | Biso mean: 38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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