+Open data
-Basic information
Entry | Database: PDB / ID: 5h59 | ||||||
---|---|---|---|---|---|---|---|
Title | Ferredoxin-NADP+ reductase from maize root | ||||||
Components | Ferredoxin--NADP reductase | ||||||
Keywords | OXIDOREDUCTASE / Flavoenzyme | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / NADPH binding / photosynthesis / chloroplast / electron transport chain / electron transfer activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Kurisu, G. / Hase, T. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Photosyn. Res. / Year: 2017 Title: Structural basis for the isotype-specific interactions of ferredoxin and ferredoxin: NADP(+) oxidoreductase: an evolutionary switch between photosynthetic and heterotrophic assimilation Authors: Shinohara, F. / Kurisu, G. / Hanke, G. / Bowsher, C. / Hase, T. / Kimata-Ariga, Y. #1: Journal: Photosyn. Res. / Year: 2004 Title: Fd : FNR Electron Transfer Complexes: Evolutionary Refinement of Structural Interactions Authors: Hanke, G.T. / Kurisu, G. / Kusunoki, M. / Hase, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5h59.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5h59.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 5h59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/5h59 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/5h59 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5h57C 5h5jC 1gawS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34876.512 Da / Num. of mol.: 1 / Fragment: UNP residues 17-327 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) References: UniProt: Q41736, UniProt: B4G043*PLUS, ferredoxin-NADP+ reductase |
---|---|
#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.12 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.2 M sodium citrate, 50 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 130708 / % possible obs: 93.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 18.6 Å2 / Net I/σ(I): 19.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GAW Resolution: 1.65→39.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1936645.01 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 45.8558 Å2 / ksol: 0.371978 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.65→39.72 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|