5J6B | pdb_00005j6b

Crystal structure of Aldehyde dehydrogenase from Burkholderia thailandensis in covelent complex with NADPH

• PDB DOI: https://doi.org/10.2210/pdb5J6B/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia thailandensis E264
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-04 Released: 2016-05-04 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.187 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Aldehyde dehydrogenase from Burkholderia thailandensis in covelent complex with NADPH

Abendroth, J., Mayclin, S.J., Lorimer, D.D., Edwards, T.E.

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: 214.28 kDa 
• Atom Count: 16,203 
• Modeled Residue Count: 1,910 
• Deposited Residue Count: 1,940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase	A, B, C, D	485	Burkholderia thailandensis E264	Mutation(s): 0  Gene Names: BTH_II0498, DR63_5272
UniProt
Find proteins for Q2T801 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T801  Go to UniProtKB:  Q2T801

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	F [auth A], H [auth B], J [auth C], L [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
CL	E [auth A], G [auth B], I [auth C], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.187 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35J6B

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.52	α = 90
b = 143.66	β = 90
c = 167.43	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary