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Yorodumi- PDB-5vw4: Nicotinamide soak of Y316S mutant of corn root ferredoxin:NADP+ r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vw4 | |||||||||
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Title | Nicotinamide soak of Y316S mutant of corn root ferredoxin:NADP+ reductase | |||||||||
Components | Ferredoxin--NADP reductase | |||||||||
Keywords | OXIDOREDUCTASE / flavoenzyme / hydride transfer / photosynthesis / active site compression | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / electron transport chain / NADPH binding / photosynthesis / chloroplast / electron transfer activity / nucleotide binding Similarity search - Function | |||||||||
Biological species | Zea mays (maize) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.351 Å | |||||||||
Authors | Kean, K.M. / Carpenter, R.A. / Hall, A.R. / Karplus, P.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: FEBS J. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vw4.cif.gz | 223 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vw4.ent.gz | 179.7 KB | Display | PDB format |
PDBx/mmJSON format | 5vw4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/5vw4 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/5vw4 | HTTPS FTP |
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-Related structure data
Related structure data | 5vw2C 5vw3C 5vw5C 5vw6C 5vw7C 5vw8C 5vw9C 5vwaC 5vwbC 3lo8S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35285.902 Da / Num. of mol.: 1 / Mutation: Y327S 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 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-FAD / |
#4: Chemical | ChemComp-NCA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.09 % |
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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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→51 Å / Num. obs: 75008 / % possible obs: 91 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 9295 / % possible all: 78.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LO8 Resolution: 1.351→51.004 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.04 / 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: 1.351→51.004 Å
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Refine LS restraints |
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LS refinement shell |
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