5UJU | pdb_00005uju

Crystal structure of NAD-dependent aldehyde dehydrogenase from Burkholderia multivorans

• PDB DOI: https://doi.org/10.2210/pdb5UJU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia multivorans ATCC 17616
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-19 Released: 2017-04-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NAD-dependent aldehyde dehydrogenase from Burkholderia multivorans

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 123.52 kDa 
• Atom Count: 9,137 
• Modeled Residue Count: 1,115 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent aldehyde dehydrogenase	A, B	576	Burkholderia multivorans ATCC 17616	Mutation(s): 0  Gene Names: BMULJ_00382 EC: 1.2.1.3
UniProt
Find proteins for A0A0H3KBY8 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KBY8  Go to UniProtKB:  A0A0H3KBY8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	F [auth A], K [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	D [auth A], E [auth A], G [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	C [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35UJU

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.43	α = 90
b = 114.43	β = 90
c = 154.52	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description