+Open data
-Basic information
Entry | Database: PDB / ID: 2gqw | ||||||
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Title | Crystal structure of Ferredoxin reductase, BphA4 (oxidized form) | ||||||
Components | ferredoxin reductase | ||||||
Keywords | OXIDOREDUCTASE / Flavoprotein | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on NAD(P)H / flavin adenine dinucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas sp. KKS102 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 1.4 Å | ||||||
Authors | Senda, T. / Senda, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin Authors: Senda, M. / Kishigami, S. / Kimura, S. / Fukuda, M. / Ishida, T. / Senda, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gqw.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gqw.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gqw_validation.pdf.gz | 711.6 KB | Display | wwPDB validaton report |
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Full document | 2gqw_full_validation.pdf.gz | 714.6 KB | Display | |
Data in XML | 2gqw_validation.xml.gz | 21 KB | Display | |
Data in CIF | 2gqw_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/2gqw ftp://data.pdbj.org/pub/pdb/validation_reports/gq/2gqw | HTTPS FTP |
-Related structure data
Related structure data | 2e4pC 2e4qC 2gr0C 2yvfC 2yvgC 2yvjC 2gqy 2gqz C: citing same article (ref.) |
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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
#1: Protein | Mass: 43221.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. KKS102 (bacteria) / Production host: Escherichia coli (E. coli) References: GenBank: 9929802, UniProt: Q52437*PLUS, ferredoxin-NADP+ reductase | ||
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#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | ChemComp-GOL / | ||
#4: Chemical | ChemComp-FMT / #5: 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: 2.76 Å3/Da / Density % sol: 55.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 2M Sodium formate, 0.1M Sodium acetate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2004 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→15 Å / Num. all: 1342357 / Num. obs: 1342357 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.4→1.47 Å / Redundancy: 14 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 5.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Difference Fourier / Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.567 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.972 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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