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- PDB-2fsv: Structure of transhydrogenase (dI.D135N.NAD+)2(dIII.E155W.NADP+)1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fsv | ||||||
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Title | Structure of transhydrogenase (dI.D135N.NAD+)2(dIII.E155W.NADP+)1 asymmetric complex | ||||||
![]() | (NAD(P) transhydrogenase subunit ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / NAD(P) TRANSHYDROGENASE SUBUNITS / NAD+ / NADP+ | ||||||
Function / homology | ![]() NAD(P)+ transhydrogenase (Si-specific) activity / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADH binding / NAD+ binding / NAD binding / NADP binding / membrane => GO:0016020 / protein dimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brondijk, T.H. / van Boxel, G.I. / Mather, O.C. / Quirk, P.G. / White, S.A. / Jackson, J.B. | ||||||
![]() | ![]() Title: The Role of Invariant Amino Acid Residues at the Hydride Transfer Site of Proton-translocating Transhydrogenase. Authors: Brondijk, T.H. / van Boxel, G.I. / Mather, O.C. / Quirk, P.G. / White, S.A. / Jackson, J.B. | ||||||
History |
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Remark 600 | LIGAND NAD 600 IS ASSOCIATED WITH TRANSHYDROGENASE DI CHAIN A. NAP 700 IS ASSOCIATED WITH ...LIGAND NAD 600 IS ASSOCIATED WITH TRANSHYDROGENASE DI CHAIN A. NAP 700 IS ASSOCIATED WITH TRANSHYDROGENASE DIII CHAIN C. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 354.6 KB | Display | ![]() |
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PDB format | ![]() | 290 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 37.2 KB | Display | |
Data in CIF | ![]() | 52.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fr8C ![]() 2frdC ![]() 1hzzS 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
-NAD(P) transhydrogenase subunit ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 40323.801 Da / Num. of mol.: 2 / Mutation: D135N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q60164, UniProt: Q2RSB2*PLUS, EC: 1.6.1.2 #2: Protein | | Mass: 21542.605 Da / Num. of mol.: 1 / Fragment: dIII domain / Mutation: E155W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q59765, UniProt: P0C188*PLUS, EC: 1.6.1.2 |
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-Non-polymers , 4 types, 387 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAD / | ||||
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#4: Chemical | #5: Chemical | ChemComp-NAP / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 16-20% 8K-PEG, 20-150 mM (NH4)2SO4,100 mM Mes pH 6.0 and 10% glycerol in the presence of 50 mM NAD+ and 5 mM NADP+, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→31.4 Å / Num. all: 50105 / Num. obs: 50105 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 43.1 Å2 / Rsym value: 0.0666 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.5 % / Num. unique all: 7207 / Rsym value: 0.34 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1HZZ Resolution: 2.3→31.37 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.868 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.366 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→31.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -14.5247 Å / Origin y: -18.7357 Å / Origin z: 25.6195 Å
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Refinement TLS group |
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