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- PDB-2yvj: Crystal structure of the ferredoxin-ferredoxin reductase (BPHA3-B... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yvj | ||||||
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Title | Crystal structure of the ferredoxin-ferredoxin reductase (BPHA3-BPHA4)complex | ||||||
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![]() | OXIDOREDUCTASE/ELECTRON TRANSPORT / electron transfer / ferredoxin / ferredoxin reductase / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX | ||||||
Function / homology | ![]() : / oxidoreductase activity, acting on NAD(P)H / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Senda, T. / Senda, M. | ||||||
![]() | ![]() Title: Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin Authors: Senda, M. / Kishigami, S. / Kimura, S. / Fukuda, M. / Ishida, T. / Senda, 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 | ![]() | 188.8 KB | Display | ![]() |
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PDB format | ![]() | 147.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 42.7 KB | Display | |
Data in CIF | ![]() | 57.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2e4pC ![]() 2e4qC ![]() 2gqwC ![]() 2gr0C ![]() 2yvfC ![]() 2yvgC 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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Unit cell |
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Components
-Protein , 2 types, 3 molecules APB
#1: Protein | Mass: 43221.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 11926.499 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 83 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FES / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES, 30%(W/V) PEG4000, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2005 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18 Å / Num. obs: 86196 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.18 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 5.46 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: THE CRYSTAL FORM IS TWINNED BY THE OPERATOR L,-K,H, PERFECT TWINED CRYSTAL.
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7044.4 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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