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Yorodumi- PDB-3w5v: Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w5v | ||||||
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Title | Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / electron transfer complex | ||||||
Function / homology | Function and homology information chloroplast thylakoid membrane protein complex / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / chloroplast stroma / response to light stimulus / photosynthesis / chloroplast / electron transport chain ...chloroplast thylakoid membrane protein complex / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / chloroplast stroma / response to light stimulus / photosynthesis / chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.81 Å | ||||||
Authors | Kimata-Ariga, Y. / Kubota-Kawai, H. / Muraki, N. / Hase, T. / Kurisu, G. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2013 Title: Concentration-dependent oligomerization of cross-linked complexes between ferredoxin and ferredoxin-NADP(+) reductase Authors: Kimata-Ariga, Y. / Kubota-Kawai, H. / Lee, Y.-H. / Muraki, N. / Ikegami, T. / Kurisu, G. / Hase, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w5v.cif.gz | 149.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w5v.ent.gz | 114.1 KB | Display | PDB format |
PDBx/mmJSON format | 3w5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w5v_validation.pdf.gz | 1012.4 KB | Display | wwPDB validaton report |
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Full document | 3w5v_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3w5v_validation.xml.gz | 29 KB | Display | |
Data in CIF | 3w5v_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/3w5v ftp://data.pdbj.org/pub/pdb/validation_reports/w5/3w5v | HTTPS FTP |
-Related structure data
Related structure data | 3w5uC 1gawS 3b2fS C: citing same article (ref.) 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 35334.477 Da / Num. of mol.: 2 / Fragment: UNP residues 42-355 / Mutation: E19C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: L-FNRI, ZEAMMB73_343560 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SLP6 #2: Protein | Mass: 10550.435 Da / Num. of mol.: 2 / Fragment: UNP residues 53-150 / Mutation: A70C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: FDX1, PFD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P27787 #3: Chemical | #4: Chemical | |
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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: 3.92 Å3/Da / Density % sol: 68.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 8% PEG 8000, 20% ethylene glycol, 100mM Bis-Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 13803 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GAW, 3B2F Resolution: 3.81→35.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 73.326 / SU ML: 0.92 / Cross valid method: THROUGHOUT / ESU R Free: 0.827 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 39.986 Å2
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Refinement step | Cycle: LAST / Resolution: 3.81→35.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.808→3.905 Å / Total num. of bins used: 20
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