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- PDB-8ito: Crystal structure of FeRlp from Desulfovibrio vulgaris (Hildenborough) -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ito | ||||||
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Title | Crystal structure of FeRlp from Desulfovibrio vulgaris (Hildenborough) | ||||||
![]() | Rubredoxin | ||||||
![]() | ELECTRON TRANSPORT / iron-sulfur cluster / metallo protein / monomer | ||||||
Function / homology | Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / iron ion binding / : / PHOSPHATE ION / Rubredoxin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nakatsuji, T. / Ogata, H. / Kitamura, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of FeRlp from Desulfovibrio vulgaris (Hildenborough) Authors: Nakatsuji, T. / Nishikawa, K. / Ogata, H. / Kitamura, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.4 KB | Display | ![]() |
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PDB format | ![]() | 29.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 8561.743 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough Gene: rdl / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.27 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.5 M NaHPO4, 0.9 M K2HPO4, 0.8 M Potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→18.68 Å / Num. obs: 52024 / % possible obs: 99.6 % / Redundancy: 6 % / Rpim(I) all: 0.039 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.01→2.04 Å / Num. unique obs: 425 / Rpim(I) all: 0.207 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→18.68 Å
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Refine LS restraints |
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LS refinement shell |
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