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- PDB-4izi: 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: 4izi | ||||||
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Title | Crystal Structure of the Alpha1 dimer of Thermus thermophilus Transhydrogenase in P4(3) | ||||||
![]() | 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 | ![]() | 285.1 KB | Display | ![]() |
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PDB format | ![]() | 232.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.4 KB | Display | ![]() |
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Full document | ![]() | 478.5 KB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 42.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4izhC ![]() 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: 3.3 Å3/Da / Density % sol: 62.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: JCSG plus kit, condition A10: 0.2 M potassium formate, 20% w/v PEG3350, pH N.A., VAPOR DIFFUSION, temperature 293K PH range: N.A. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2011 / 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: 2.4→38.37 Å / Num. all: 39298 / Num. obs: 39243 / % possible obs: 99.86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 57.79 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.4→2.462 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 1.1 / Num. unique all: 6432 / Rsym value: 0.469 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L7D Resolution: 2.4→38.37 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.213 / SU ML: 0.138 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.293 / ESU R Free: 0.24 / 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: 62.691 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→38.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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