5JRY | pdb_00005jry

Crystal structure of a NAD-dependent Aldehyde dehydrogenase from Burkholderia multivorans in covalent complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb5JRY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia multivorans ATCC 17616
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-06 Released: 2016-06-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.130 (Depositor), 0.132 (DCC) 
• R-Value Work: 
  0.113 (Depositor), 0.114 (DCC) 
• R-Value Observed: 
  0.113 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a NAD-dependent Aldehyde dehydrogenase from Burkholderia multivorans

Abendroth, J., Dranow, D.M., Lorimer, D.D., Edewards, 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: 53.78 kDa 
• Atom Count: 4,496 
• Modeled Residue Count: 477 
• Deposited Residue Count: 485 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent aldehyde dehydrogenase	A	485	Burkholderia multivorans ATCC 17616	Mutation(s): 0  Gene Names: BMULJ_03565 EC: 1.2.1
UniProt
Find proteins for A0A0H3KPC8 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KPC8  Go to UniProtKB:  A0A0H3KPC8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.130 (Depositor), 0.132 (DCC) 
• R-Value Work:  0.113 (Depositor), 0.114 (DCC) 
• R-Value Observed: 0.113 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35JRY

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.08	α = 90
b = 87.03	β = 90
c = 124.59	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description