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- PDB-5vwb: Y316F mutant of corn root ferredoxin:NADP+ reductase in alternate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vwb | |||||||||
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Title | Y316F mutant of corn root ferredoxin:NADP+ reductase in alternate space group | |||||||||
![]() | Ferredoxin--NADP reductase | |||||||||
![]() | OXIDOREDUCTASE / flavoenzyme / hydride transfer / photosynthesis / active site compression | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Kean, K.M. / Carpenter, R.A. / Hall, A.R. / Karplus, P.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution studies of hydride transfer in the ferredoxin:NADP(+) reductase superfamily. Authors: Kean, K.M. / Carpenter, R.A. / Pandini, V. / Zanetti, G. / Hall, A.R. / Faber, R. / Aliverti, A. / Karplus, P.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 217 KB | Display | ![]() |
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PDB format | ![]() | 184.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1019.9 KB | Display | ![]() |
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Full document | ![]() | 1023.9 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vw2C ![]() 5vw3C ![]() 5vw4C ![]() 5vw5C ![]() 5vw6C ![]() 5vw7C ![]() 5vw8C ![]() 5vw9C ![]() 5vwaC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 35345.996 Da / Num. of mol.: 1 / Mutation: Y361F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q41736, UniProt: B4G043*PLUS, ferredoxin-NADP+ reductase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-FAD / |
#4: Chemical | ChemComp-NAP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 22-24% PEG 8000, 0.1 M sodium cacodylate (pH 6-7), 0.18-0.22 M magnesium acetate, 100 mM nicotinamide |
-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10.834 Å / Num. obs: 32137 / % possible obs: 88.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 1 / Num. unique obs: 1058 / % possible all: 30 |
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Processing
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Refinement | Resolution: 1.8→10.834 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10.834 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 31.6866 Å / Origin y: -24.5376 Å / Origin z: 14.4353 Å
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Refinement TLS group | Selection details: all |