4TWR | pdb_00004twr

Structure of UDP-glucose 4-epimerase from Brucella abortus

• PDB DOI: https://doi.org/10.2210/pdb4TWR/pdb

• Classification: ISOMERASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2014-07-01 Released: 2014-10-08 
• Deposition Author(s): Horanyi, P.S., Abendroth, J., Lorimer, D., Edwards, T., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Structure of UDP-glucose 4-epimerase from Brucella melitensis

Horanyi, P.S., Abendroth, J., Lorimer, D., Edwards, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 36.99 kDa 
• Atom Count: 2,689 
• Modeled Residue Count: 325 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase	A	336	Brucella abortus 2308	Mutation(s): 0  Gene Names: galE-2, BAB2_0694 EC: 5.1.3.2
UniProt
Find proteins for Q2YKG6 (Brucella abortus (strain 2308)) Explore Q2YKG6  Go to UniProtKB:  Q2YKG6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34TWR

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.6	α = 90
b = 86.11	β = 90
c = 126.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Horanyi, P.S., Abendroth, J., Lorimer, D., Edwards, T., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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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: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Refinement description