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Yorodumi- PDB-5ygq: Crystal Structure of Ferredoxin NADP+ Oxidoreductase from Rhodops... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ygq | ||||||
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Title | Crystal Structure of Ferredoxin NADP+ Oxidoreductase from Rhodopseudomonas palustris | ||||||
Components | Ferredoxin--NADP reductase | ||||||
Keywords | OXIDOREDUCTASE / electron transport / fad / flavoprotein / nadp | ||||||
Function / homology | Function and homology information ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Muraki, N. / Seo, D. / Kurisu, G. | ||||||
Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2019 Title: Kinetic and structural insight into a role of the re-face Tyr328 residue of the homodimer type ferredoxin-NADP+oxidoreductase from Rhodopseudomonas palustris in the reaction with NADP+/NADPH. Authors: Seo, D. / Muraki, N. / Kurisu, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ygq.cif.gz | 269.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ygq.ent.gz | 217.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ygq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ygq_validation.pdf.gz | 938.1 KB | Display | wwPDB validaton report |
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Full document | 5ygq_full_validation.pdf.gz | 952.1 KB | Display | |
Data in XML | 5ygq_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 5ygq_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/5ygq ftp://data.pdbj.org/pub/pdb/validation_reports/yg/5ygq | HTTPS FTP |
-Related structure data
Related structure data | 3ab1S S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 3 - 341 / Label seq-ID: 3 - 341
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-Components
#1: Protein | Mass: 37055.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic) Strain: ATCC BAA-98 / CGA009 / Gene: RPA3954 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N2U4, ferredoxin-NADP+ reductase #2: Chemical | #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: 2.37 Å3/Da / Density % sol: 48.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, ammonium iodide, Tris-HCl pH8.5 |
-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: Apr 22, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 27560 / % possible obs: 98.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.3 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ab1 Resolution: 2.4→36.42 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.893 / SU B: 23.465 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.645 / ESU R Free: 0.302 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.45 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→36.42 Å
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Refine LS restraints |
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