[English] 日本語
![](img/lk-miru.gif)
- PDB-2frd: Structure of Transhydrogenase (dI.S138A.NADH)2(dIII.NADPH)1 asymm... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2frd | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Transhydrogenase (dI.S138A.NADH)2(dIII.NADPH)1 asymmetric complex | ||||||
![]() |
| ||||||
![]() | OXIDOREDUCTASE / NAD(P) TRANSHYDROGENASE SUBUNITS / NADH / NADPH | ||||||
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 |
| ||||||
Remark 600 | LIGAND NAD 500 IS ASSOCIATED WITH TRANSHYDROGENASE DI CHAIN A. NAD 600 IS ASSOCIATED WITH ...LIGAND NAD 500 IS ASSOCIATED WITH TRANSHYDROGENASE DI CHAIN A. NAD 600 IS ASSOCIATED WITH TRANSHYDROGENASE DI CHAIN B. NAP 300 IS ASSOCIATED WITH TRANSHYDROGENASE DIII CHAIN C. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 349.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 286.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 43.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fr8C ![]() 2fsvC ![]() 1hzzS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 40308.785 Da / Num. of mol.: 2 / Mutation: S138A 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: 21485.510 Da / Num. of mol.: 1 / Fragment: dIII domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q59765, UniProt: P0C188*PLUS, EC: 1.6.1.2 #3: Chemical | #4: Chemical | ChemComp-NDP / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.65 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 22-24% 8K-PEG, 60-140 mM (NH4)2SO4, 100 mM Mes, pH 6.0 and 10% glycerol in the presence of 50 mM NADH and 5 mM NADPH, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→45.93 Å / Num. all: 18400 / Num. obs: 18400 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 75.5 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4 / Num. unique all: 2660 / % possible all: 99.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 1HZZ Resolution: 3.2→45.93 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.884 / SU B: 60.628 / SU ML: 0.466 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.575 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 43.582 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→45.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -14.686 Å / Origin y: -19.365 Å / Origin z: 25.665 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|