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- PDB-4izh: Crystal Structure of the Alpha1 dimer of Thermus thermophilus Tra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4izh | ||||||
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Title | Crystal Structure of the Alpha1 dimer of Thermus thermophilus Transhydrogenase in P6 | ||||||
![]() | NAD/NADP transhydrogenase alpha subunit 1 | ||||||
![]() | OXIDOREDUCTASE / Alpha1 subunit / NAD binding / Domain III of Beta subunit | ||||||
Function / homology | ![]() : / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stout, C.D. / Yamaguchi, M. / Leung, J. | ||||||
![]() | ![]() Title: Crystal structure analysis of Thermus thermophilus transhydrogenase soluble domains Authors: Leung, J. / Yamaguchi, M. / Schurig Briccio, L.A. / B Gennis, R. / Stout, C.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.9 KB | Display | ![]() |
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PDB format | ![]() | 120.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.6 KB | Display | ![]() |
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Full document | ![]() | 478.7 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4iziC ![]() 4j16C ![]() 4j1tC ![]() 1l7dS S: Starting model for refinement C: citing same article ( |
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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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Details | Dimer of alpha1 subunit |
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Components
#1: Protein | Mass: 40851.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 3.5 Details: MemStart MemSys kit, condition E2: 0.1M Sodium chloride, 0.1M Na citrate pH 3.5, 0.1M Lithium sulphate, 30% v/v PEG 400, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2012 / Details: Rh coated flat mirror |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, Si(111); asymmetric cut 4.965 degs. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→140.61 Å / Num. all: 98204 / Num. obs: 97773 / % possible obs: 99.52 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 25.81 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 5 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.7 / Num. unique all: 15023 / Rsym value: 0.437 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L7D Resolution: 1.8→140.61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.706 / SU ML: 0.071 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.018 / ESU R Free: 0.017 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.759 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→140.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.796→1.843 Å / Total num. of bins used: 20
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