4FKZ

Crystal structure of Bacillus subtilis UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP

• PDB DOI: https://doi.org/10.2210/pdb4FKZ/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-14 Released: 2013-05-08 
• Deposition Author(s): Yang, C.S., Chen, S.C., Kuan, S.M., Chen, Y.R., Liu, Y.H., Chen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.199 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

Crystal structure of Bacillus subtilis UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP

Yang, C.S., Chen, S.C., Kuan, S.M., Chen, Y.R., Liu, Y.H., Chen, Y.

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: 89.55 kDa 
• Atom Count: 7,153 
• Modelled Residue Count: 760 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 2-epimerase	A, B	388	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: BSU35660, mnaA EC: 5.1.3.14
UniProt
Find proteins for P39131 (Bacillus subtilis (strain 168)) Explore P39131  Go to UniProtKB:  P39131

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD1	C [auth A], E [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-CFRASDGPSA-N
UDP	D [auth A], F [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.199 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.289	α = 90
b = 209.338	β = 90
c = 46.81	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Yang, C.S., Chen, S.C., Kuan, S.M., Chen, Y.R., Liu, Y.H., Chen, Y.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description