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Yorodumi- PDB-2vnk: X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBAC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vnk | ||||||
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Title | X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH NADP. FORM III AT 1.93 ANGSTROMS RESOLUTION | ||||||
Components | NADPH\:FERREDOXIN REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSFER / RHODOBACTER CAPSULATUS / FERREDOXIN(FLAVODOXIN)-NADP(H) REDUCTASE / NADP / FLAVOPROTEINS | ||||||
Function / homology | Function and homology information flavodoxin-NADP+ reductase / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | RHODOBACTER CAPSULATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Perez-Dorado, I. / Hermoso, J.A. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2009 Title: Coenzyme Binding and Hydride Transfer in Rhodobacter Capsulatus Ferredoxin/Flavodoxin Nadp(H) Oxidoreductase. Authors: Bortolotti, A. / Perez-Dorado, I. / Goni, G. / Medina, M. / Hermoso, J.A. / Carrillo, N. / Cortez, N. #1: Journal: Biochemistry / Year: 2005 Title: The Feredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus: Molecular Structure and Catalytic Mechanism Authors: Nogues, I. / Perez-Dorado, I. / Frago, S. / Bittel, C. / Mayhew, S. / Gomez-Moreno, C. / Hermoso, J.A. / Medina, M. / Cortez, N. / Carrillo, N. #2: 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, I. / Bittel, C. / Cortez, N. / Hermoso, J.A. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vnk.cif.gz | 237.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vnk.ent.gz | 190.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/2vnk ftp://data.pdbj.org/pub/pdb/validation_reports/vn/2vnk | HTTPS FTP |
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-Related structure data
Related structure data | 2vnhC 2vniC 2vnjC 2bgiS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 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: Chemical | ChemComp-NAP / #4: 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: 2.83 Å3/Da / Density % sol: 56.6 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→49.21 Å / Num. obs: 122712 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.93→2.12 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.2 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BGI Resolution: 1.93→49.21 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT Details: THE FIRST 15 RESIDUES OF THE POLYPEPTIDE CHAIN AND THE NMN MOIETY OF THE NADP ARE NOT INCLUDED IN THE CHAINS A, B, C AND D OF THE MODEL DUE TO THEY ARE NOT OBSERVED IN THE ELECTRON DENSITY ...Details: THE FIRST 15 RESIDUES OF THE POLYPEPTIDE CHAIN AND THE NMN MOIETY OF THE NADP ARE NOT INCLUDED IN THE CHAINS A, B, C AND D OF THE MODEL DUE TO THEY ARE NOT OBSERVED IN THE ELECTRON DENSITY MAP. RESIDUES 270-272 OF CHAINS B AND D ARE NOT INCLUDED IN THE MODEL DUE TO POOR QUALITY OF THE ELECTRON DENSITY MAP IN THESE POSITIONS.
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.772 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→49.21 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20 /
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