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- PDB-2bgi: X-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bgi | ||||||
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Title | X-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus complexed with three molecules of the detergent n-heptyl- beta-D-thioglucoside at 1.7 Angstroms | ||||||
![]() | FERREDOXIN-NADP(H) REDUCTASE | ||||||
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Function / homology | ![]() flavodoxin-NADP+ reductase / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perez-Dorado, J.I. / Hermoso, J.A. / Nogues, I. / Frago, S. / Bittel, C. / Mayhew, S.G. / Gomez-Moreno, C. / Medina, M. / Cortez, N. / Carrillo, N. | ||||||
![]() | ![]() Title: The Ferredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus: Molecular Structure and Catalytic Mechanism Authors: Nogues, I. / Perez-Dorado, J.I. / Frago, S. / Bittel, C. / Mayhew, S.G. / Gomez-Moreno, C. / Hermoso, J.A. / Medina, M. / Cortez, N. / Carrillo, N. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Ferredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus Authors: Perez-Dorado, J.I. / Bittel, C. / Cortez, N. / Hermoso, J.A. #2: Journal: FEBS Lett. / Year: 2003 Title: The Oxidant-Responsive Diaphorase of Rhodobacter Capsulatus is a Ferredoxin (Flavodoxin)-Nadp(H) Reductase Authors: Bittel, C. / Tabares, L.C. / Armesto, M. / Carrillo, N. / Cortez, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.6 KB | Display | ![]() |
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PDB format | ![]() | 54.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2bgjC ![]() 1a8pS C: citing same article ( S: Starting model for refinement |
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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 / Sugars , 2 types, 4 molecules A![](data/chem/img/HTG.gif)
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#1: Protein | Mass: 30436.889 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#3: Sugar |
-Non-polymers , 4 types, 268 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / ![]() | ||
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#4: Chemical | ChemComp-SO4 / ![]() | ||
#5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 64 % |
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Crystal grow![]() | pH: 6.5 / Details: pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 17, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→45.6 Å / Num. obs: 61984 / % possible obs: 97.2 % / Observed criterion σ(I): 4 / Redundancy: 7.3 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1A8P Resolution: 1.68→45.64 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1767576.25 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 1 - 15 HAVE NOT BEEN MODELED BECAUSE THEY ARE NOT DEFINED IN THE ELECTRON DENSITY MAP
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.8594 Å2 / ksol: 0.389103 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.68→45.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.79 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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