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- PDB-2rdv: RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2rdv | ||||||
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Title | RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRYSTAL FORM | ||||||
![]() | RUBREDOXIN | ||||||
![]() | ELECTRON TRANSFER / RUBREDOXIN / COMPND / ELECTRON TRANSFER PROTEIN / METALLOPROTEIN / SULFATE-REDUCING BACTERIUM | ||||||
Function / homology | ![]() alkane catabolic process / electron transfer activity / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Higuchi, Y. / Yasuoka, N. | ||||||
![]() | ![]() 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: ![]() Title: Preliminary Crystallographic Study of Two Crystal Forms of Rubredoxin from Sulfate-Reducing Bactrium Authors: Higuchi, Y. / Sugiyama, M.S. / Morimoto, S. / Ogata, Y. / Yagi, M. / Yasuoka, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.6 KB | Display | ![]() |
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PDB format | ![]() | 28.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.7 KB | Display | ![]() |
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Full document | ![]() | 379.1 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rdvSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 5602.237 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: IAM 12604 Source: (natural) ![]() Species: Desulfovibrio vulgaris / Strain: MIYAZAKI F / References: UniProt: P15412 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.2 % | |||||||||||||||||||||||||
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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: ![]() ![]() ![]() |
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: 1.9→20 Å / Num. obs: 53316 / % possible obs: 82.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.111 |
Reflection | *PLUS Num. obs: 9604 / Observed criterion σ(I): 3 / Num. measured all: 53316 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RDV Resolution: 1.9→20 Å / Isotropic thermal model: RESTRAINED / σ(F): 3
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Displacement parameters | Biso mean: 14.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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