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Yorodumi- PDB-5vw9: Nicotinamide soak of Y316S mutant of corn root ferredoxin:NADP+ r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vw9 | |||||||||
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Title | Nicotinamide soak of Y316S mutant of corn root ferredoxin:NADP+ reductase in alternate space group | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.894 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 | 5vw9.cif.gz | 220 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vw9.ent.gz | 178.6 KB | Display | PDB format |
PDBx/mmJSON format | 5vw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/5vw9 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/5vw9 | HTTPS FTP |
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-Related structure data
Related structure data | 5vw2C 5vw3C 5vw4C 5vw5C 5vw6C 5vw7C 5vw8C 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 417 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-FAD / |
#4: Chemical | ChemComp-NCA / |
#5: Chemical | ChemComp-ACT / |
#6: 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 % |
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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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 17, 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: 1.9→11.48 Å / Num. obs: 29752 / % possible obs: 97.6 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 2603 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LO8 Resolution: 1.894→11.478 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.3 / 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: 1.894→11.478 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: 27.042 Å / Origin y: -25.0801 Å / Origin z: 15.9536 Å
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Refinement TLS group | Selection details: all |