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- PDB-5vw3: NADP+ soak of Y316S mutant of corn root ferredoxin:NADP+ reductase -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vw3 | |||||||||
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Title | NADP+ soak of Y316S mutant of corn root ferredoxin:NADP+ reductase | |||||||||
![]() | Ferredoxin--NADP reductase | |||||||||
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Function / homology | ![]() oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 228 KB | Display | ![]() |
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PDB format | ![]() | 183.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5vw2C ![]() 5vw4C ![]() 5vw5C ![]() 5vw6C ![]() 5vw7C ![]() 5vw8C ![]() 5vw9C ![]() 5vwaC ![]() 5vwbC ![]() 3lo8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: Y316A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q41736, UniProt: B4G043*PLUS, ![]() |
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-Non-polymers , 5 types, 495 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-FAD / ![]() |
#4: Chemical | ChemComp-NAP / ![]() |
#5: Chemical | ChemComp-ACT / ![]() |
#6: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.65 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.45→50.93 Å / Num. obs: 65831 / % possible obs: 97.9 % / Redundancy: 9.6 % / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3 / Num. unique obs: 8739 / Rpim(I) all: 0.024 / % possible all: 91.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3LO8 Resolution: 1.453→50.93 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.1 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: 1.453→50.93 Å
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Refine LS restraints |
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LS refinement shell |
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