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- PDB-9bkp: Crystal structure of rubredoxin from Pyrococcus furiosus reconsti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9bkp | ||||||
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Title | Crystal structure of rubredoxin from Pyrococcus furiosus reconstituted with FeCl3 solved by Fe/S-SAD | ||||||
![]() | Rubredoxin | ||||||
![]() | ELECTRON TRANSPORT / Cobalt substituted / native SAD | ||||||
Function / homology | ![]() alkane catabolic process / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of rubredoxin from Pyrococcus furiosus reconstituted with FeCl3 solved by Fe/S-SAD Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29.4 KB | Display | ![]() |
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PDB format | ![]() | 14.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 806.2 KB | Display | ![]() |
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Full document | ![]() | 806.2 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 6031.728 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.4, 2.2M ammonium sulfate, 30% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 4900 / % possible obs: 96.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 9.78 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 84.73 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 35.3 / Num. unique obs: 164 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.73 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→27.03 Å
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Refine LS restraints |
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LS refinement shell |
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