4U3W | pdb_00004u3w

X-ray crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase from Burkholderia cenocepacia

• PDB DOI: https://doi.org/10.2210/pdb4U3W/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia cenocepacia J2315
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-23 Released: 2014-07-30 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase from Burkholderia cenocepacia

Fairman, J.W., Dranow, D.M., Lorimer, 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 109.06 kDa 
• Atom Count: 8,113 
• Modeled Residue Count: 969 
• Deposited Residue Count: 1,010 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-aminomuconate 6-semialdehyde dehydrogenase	A, B	505	Burkholderia cenocepacia J2315	Mutation(s): 0  Gene Names: nbaE, BCAM2132
UniProt
Find proteins for B4EFS9 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EFS9  Go to UniProtKB:  B4EFS9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34U3W

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.75	α = 90
b = 87.69	β = 128.31
c = 111.88	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
XDS	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2014-08-06
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description