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- PDB-5gtk: NAD+ complex structure of aldehyde dehydrogenase from bacillus cereus -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gtk | |||||||||
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Title | NAD+ complex structure of aldehyde dehydrogenase from bacillus cereus | |||||||||
![]() | Betaine-aldehyde dehydrogenase | |||||||||
![]() | OXIDOREDUCTASE / Aldehyde Dehydrogenase NAD+ / NADP+ | |||||||||
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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 387.3 KB | Display | ![]() |
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PDB format | ![]() | 315.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5gtlC ![]() 4ps9 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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Unit cell |
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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-NAD / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.19 % |
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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 |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2012 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 67318 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 63.1 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 7 % / Rmerge(I) obs: 0.08 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PS9 ![]() 4ps9 Resolution: 2.6→47.93 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.875 / SU B: 9.163 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 2.462 / ESU R Free: 0.308 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.868 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→47.93 Å
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Refine LS restraints |
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