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Yorodumi- PDB-5vw2: NADPH soak of Y316S mutant of corn root ferredoxin:NADP+ reductase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vw2 | |||||||||
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Title | NADPH soak of Y316S mutant of corn root ferredoxin:NADP+ reductase | |||||||||
Components | Ferredoxin--NADP reductase | |||||||||
Keywords | OXIDOREDUCTASE / flavoenzyme / hydride transfer / photosynthesis / active site compression / TRANSFERASE | |||||||||
Function / homology | Function and homology information 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 | Zea mays (maize) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 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 | 5vw2.cif.gz | 232.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vw2.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 5vw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/5vw2 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/5vw2 | HTTPS FTP |
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-Related structure data
Related structure data | 5vw3C 5vw4C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35285.902 Da / Num. of mol.: 1 / Mutation: Y316S 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, 504 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-FDA / |
#5: Chemical | ChemComp-NAP / |
#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: 2.65 Å3/Da / Density % sol: 53.64 % |
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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: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50.96 Å / Num. obs: 66408 / % possible obs: 98.1 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8907 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LO8 Resolution: 1.451→50.96 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.53 Details: Atoms C5D, C4D, O4D, C3D, O3D, C2D, O2D, N1N, and C1D of NAP modeled as 0.60 (A) and 0.40 (B) occupancy where alternate conformation is visible. All other atoms modeled as 1.0 (A) and 0.0 (B) ...Details: Atoms C5D, C4D, O4D, C3D, O3D, C2D, O2D, N1N, and C1D of NAP modeled as 0.60 (A) and 0.40 (B) occupancy where alternate conformation is visible. All other atoms modeled as 1.0 (A) and 0.0 (B) to reflect only one visible conformation for the remainder of NAP.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.451→50.96 Å
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Refine LS restraints |
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LS refinement shell |
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