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Yorodumi- PDB-2bgj: X-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bgj | ||||||
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Title | X-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus at 2.1 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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, 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 | 2bgj.cif.gz | 219.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bgj.ent.gz | 178.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bgj_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 2bgj_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 2bgj_validation.xml.gz | 44.3 KB | Display | |
Data in CIF | 2bgj_validation.cif.gz | 59.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/2bgj ftp://data.pdbj.org/pub/pdb/validation_reports/bg/2bgj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 30436.889 Da / Num. of mol.: 4 / 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 #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % Description: STARTING MODEL USED FOR THE MOLECULAR REPLACEMENT WAS THE REFINED FPR MODEL OBTAINED IN PRESENCE OF THE DETERGENT N- HEPTYL-BETA-DTHIOGLUCOSIDE |
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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: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 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: 2.1→22.8 Å / Num. obs: 73447 / % possible obs: 80.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.1→2.3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.3 / % possible all: 60.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→105.41 Å / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.148 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→105.41 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev Biso : 0.84 Å2 / Rms dev position: 0.46 Å / Weight Biso : 2 / Weight position: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20 /
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