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- PDB-1pt9: Crystal Structure Analysis of the DIII Component of Transhydrogen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pt9 | ||||||
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Title | Crystal Structure Analysis of the DIII Component of Transhydrogenase with a Thio-Nicotinamide Nucleotide Analogue | ||||||
![]() | NAD(P) transhydrogenase, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / Transhydrogenase / thio-nicotinamide / mitochondria / proton translocation | ||||||
Function / homology | ![]() response to vitamin / NAD(P)+ transhydrogenase (Si-specific) activity / : / cellular oxidant detoxification / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / Citric acid cycle (TCA cycle) / intracellular oxygen homeostasis / positive regulation of hydrogen peroxide catabolic process / : ...response to vitamin / NAD(P)+ transhydrogenase (Si-specific) activity / : / cellular oxidant detoxification / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / Citric acid cycle (TCA cycle) / intracellular oxygen homeostasis / positive regulation of hydrogen peroxide catabolic process / : / positive regulation of mitochondrial membrane potential / proton transmembrane transport / tricarboxylic acid cycle / reactive oxygen species metabolic process / negative regulation of protein phosphorylation / cell redox homeostasis / NAD binding / NADP binding / mitochondrial inner membrane / negative regulation of apoptotic process / mitochondrion / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, A. / Venning, J.D. / Quirk, P.G. / van Boxel, G.I. / Rodrigues, D.J. / White, S.A. / Jackson, J.B. | ||||||
![]() | ![]() Title: Interactions between transhydrogenase and thio-nicotinamide analogues of NAD(H) and NADP(H) underline the importance of nucleotide conformational changes in coupling to proton translocation Authors: Singh, A. / Venning, J.D. / Quirk, P.G. / Van Boxel, G.I. / Rodrigues, D.J. / White, S.A. / Jackson, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.4 KB | Display | ![]() |
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PDB format | ![]() | 66.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1023.2 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ptjC ![]() 1djlS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22281.652 Da / Num. of mol.: 2 / Fragment: residues 880-1086 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.98 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 Details: ammonium sulfate, peg 400, glycerol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 100K |
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: unpublished data, White, S.A., (2000) Structure Fold.Des., 8, 1. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.42→36.82 Å / Num. all: 102352 / Num. obs: 100817 / % possible obs: 98.5 % / Biso Wilson estimate: 50.91 Å2 / Rsym value: 0.077 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.42→2.55 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 2312 / Rsym value: 0.319 / % possible all: 96.2 |
Reflection | *PLUS Num. obs: 16825 / Redundancy: 6 % / Num. measured all: 100817 / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS % possible obs: 96.2 % / Redundancy: 4.9 % / Num. unique obs: 2312 / Num. measured obs: 11365 / Rmerge(I) obs: 0.319 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DJL Resolution: 2.42→36.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38.71 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→36.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.45 Å
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Xplor file |
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Refinement | *PLUS Lowest resolution: 36.82 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.2187 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |