+Open data
-Basic information
Entry | Database: PDB / ID: 2yvf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ferredoxin reductase BPHA4 (hydroquinone) | ||||||
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. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yvf.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yvf.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yvf_validation.pdf.gz | 1008.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2yvf_full_validation.pdf.gz | 1015.1 KB | Display | |
Data in XML | 2yvf_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 2yvf_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yvf ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yvf | HTTPS FTP |
-Related structure data
Related structure data | 2e4pC 2e4qC 2gqwC 2gr0C 2yvgC 2yvjC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43221.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: strain KKS102 / Gene: bphA4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52437, ferredoxin-NADP+ reductase | ||
---|---|---|---|
#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | ChemComp-NAD / | ||
#4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.34 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 2M SODIUM FORMATE, 0.1M SODIUM ACETATE, pH 5.40, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9792 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 17, 2005 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→15 Å / Num. obs: 60816 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.54 |
Reflection shell | Resolution: 1.6→1.68 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 3.1 / % possible all: 94.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.191 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 29.59 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|