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Yorodumi- PDB-2bgi: X-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobac... -
+Open data
-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 | ||||||
Components | FERREDOXIN-NADP(H) REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FERREDOXIN(FLAVODOXIN)-NADP(H) REDUCTASE / FLAVOPROTEINS / ELECTRON TRANSFER / RHODOBACTER CAPSULATUS | ||||||
Function / homology | Function and homology information flavodoxin-NADP+ reductase / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / heme catabolic process / cellular response to oxidative stress / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | RHODOBACTER CAPSULATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Biochemistry / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bgi.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bgi.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bgi_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2bgi_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2bgi_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 2bgi_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/2bgi ftp://data.pdbj.org/pub/pdb/validation_reports/bg/2bgi | HTTPS FTP |
-Related structure data
Related structure data | 2bgjC 1a8pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules A
#1: Protein | Mass: 30436.889 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Strain: 37B4 / Variant: DSM938 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9L6V3, ferredoxin-NADP+ reductase |
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#3: Sugar |
-Non-polymers , 4 types, 268 molecules
#2: Chemical | ChemComp-FAD / | ||
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#4: Chemical | ChemComp-SO4 / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
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: 0.934 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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