[English] 日本語

- PDB-5gtl: NADPH complex structure of Aldehyde Dehydrogenase from Bacillus cereus -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5gtl | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | NADPH complex structure of Aldehyde Dehydrogenase from Bacillus cereus | |||||||||
![]() | Betaine-aldehyde dehydrogenase | |||||||||
![]() | OXIDOREDUCTASE / Aldehyde Dehydrogenase NAPDH-COMPLEX STRUCTURE NADPH ROSSMANN 2 FOLD | |||||||||
Function / homology | ![]() aldehyde dehydrogenase [NAD(P)+] / aldehyde dehydrogenase [NAD(P)+] activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ngo, H.P.T. / Hong, S.H. / Ho, T.H. / Oh, D.K. / Kang, L.W. | |||||||||
![]() | ![]() Title: Crystal structures of aldehyde dehydrogenase from Bacillus cereus having atypical bidirectional oxidizing and reducing activities for all-trans-retinal Authors: Ngo, H.P.T. / Hong, S.H. / Ho, T.H. / Oh, D.K. / Kang, L.W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 419.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 339 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 86.1 KB | Display | |
Data in CIF | ![]() | 125.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gtkC ![]() 4ps9 C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 54216.277 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-NDP / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.87 % |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.15M DL MALIC ACID PH 7.0, 18% PEG 3350 (W/V) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2013 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 149308 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 42.8 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 6.4 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4PS9 ![]() 4ps9 Resolution: 2→47.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.211 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.176 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.964 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→47.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|