5GTK | pdb_00005gtk

NAD+ complex structure of aldehyde dehydrogenase from bacillus cereus

• PDB DOI: https://doi.org/10.2210/pdb5GTK/pdb
• Entry: 5GTK supersedes: 4PT0

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus cereus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-21 Released: 2017-09-06 
• Deposition Author(s): Ngo, H.P.T., Hong, S.H., Ho, T.H., Oh, D.K., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of aldehyde dehydrogenase from Bacillus cereus having atypical bidirectional oxidizing and reducing activities for all-trans-retinal

Ngo, H.P.T., Hong, S.H., Ho, T.H., Oh, D.K., Kang, L.W.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 219.59 kDa 
• Atom Count: 15,843 
• Modeled Residue Count: 1,959 
• Deposited Residue Count: 1,976 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Betaine-aldehyde dehydrogenase	A, B, C, D	494	Bacillus cereus	Mutation(s): 0  Gene Names: AT268_22120

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], G [auth B], I [auth C], J [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
NA	F [auth A], H [auth B], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.222	α = 90
b = 93.253	β = 97.86
c = 145.149	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Ngo, H.P.T., Hong, S.H., Ho, T.H., Oh, D.K., Kang, L.W.
• This entry supersedes: 4PT0

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2018-02-07
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description