3EHE | pdb_00003ehe

Crystal structure of UDP-glucose 4 epimerase (galE-1) from Archaeoglobus fulgidus

• PDB DOI: https://doi.org/10.2210/pdb3EHE/pdb

• Classification: ISOMERASE
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-12 Released: 2008-10-14 
• Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.287 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Literature

Crystal structure of galE-1 from Archaeoglobus fulgidus

Agarwal, R., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.87 kDa 
• Atom Count: 4,863 
• Modeled Residue Count: 580 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 4-epimerase (GalE-1)	A, B	313	Archaeoglobus fulgidus	Mutation(s): 0  Gene Names: AF_0361
UniProt
Find proteins for O29886 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29886  Go to UniProtKB:  O29886

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.287 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.574	α = 90
b = 55.529	β = 97.52
c = 89.634	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building
Coot	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references