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- PDB-2wc1: Three-dimensional Structure of the Nitrogen Fixation Flavodoxin (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wc1 | ||||||
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Title | Three-dimensional Structure of the Nitrogen Fixation Flavodoxin (NifF) from Rhodobacter capsulatus at 2.2 A | ||||||
![]() | FLAVODOXIN | ||||||
![]() | ELECTRON TRANSPORT / FLAVOPROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Perez-Dorado, I. / Bittel, C. / Hermoso, J.A. / Cortez, N. / Carrillo, N. | ||||||
![]() | ![]() Title: Structural and Phylogenetic Analysis of Rhodobacter Capsulatus Niff: Uncovering General Features of Nitrogen-Fixation (Nif)-Flavodoxins. Authors: Perez-Dorado, I. / Bortolotti, A. / Cortez, N. / Hermoso, J.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Crystallization of a Flavodoxin Involved in Nitrogen Fixation in Rhodobacter Capsulatus. Authors: Perez-Dorado, I. / Bortolotti, A. / Cortez, N. / Hermoso, J.A. #2: ![]() Title: The Ferredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus: Molecular Structure and Catalytic Mechanism. Authors: Nogues, I. / Perez-Dorado, I. / Frago, S. / Bittel, C. / Mayhew, S.G. / Gomez-Moreno, C. / Hermoso, J.A. / Medina, M. / Cortez, N. / Carrillo, N. #3: 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. #4: Journal: Biochim.Biophys.Acta / Year: 1998 Title: Stopped-Flow Kinetic Studies of Low Potential Electron Carriers of the Photosynthetic Bacterium, Rhodobacter Capsulatus: Ferredoxin I and Niff. Authors: Hallenbeck, P.C. / Gennaro, G. #5: Journal: J.Bacteriol. / Year: 1996 Title: Cloning, Characterization, and Regulation of Niff from Rhodobacter Capsulatus. Authors: Gennaro, G. / Hubner, P. / Sandmeier, U. / Yakunin, A.F. / Hallenbeck, P.C. #6: Journal: J.Bacteriol. / Year: 1993 Title: Purification and Properties of a Nif-Specific Flavodoxin from the Photosynthetic Bacterium Rhodobacter Capsulatus. Authors: Yakunin, A.F. / Gennaro, G. / Hallenbeck, P.C. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.3 KB | Display | ![]() |
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PDB format | ![]() | 36 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 780.6 KB | Display | ![]() |
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Full document | ![]() | 784.6 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1flvS 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
#1: Protein | Mass: 19834.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.7 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 25, 2004 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25.7 Å / Num. obs: 24830 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 22.4 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 26 |
Reflection shell | Resolution: 2.2→2.4 Å / Redundancy: 22.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 8.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FLV Resolution: 2.17→25.66 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1425280.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.1858 Å2 / ksol: 0.414581 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.17→25.66 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.17→2.31 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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