3RUF | pdb_00003ruf

Alternative analogs as viable substrates of UDP-hexose 4-epimerases

• PDB DOI: https://doi.org/10.2210/pdb3RUF/pdb

• Classification: ISOMERASE
• Organism(s): Plesiomonas shigelloides
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-05 Released: 2011-05-25 
• Deposition Author(s): Bhatt, V.S., Guan, W., Wang, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Alternative analogs as viable substrates of UDP-hexose 4-epimerases

Bhatt, V.S., Guan, W., Wang, P.G.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 163.65 kDa 
• Atom Count: 11,427 
• Modeled Residue Count: 1,344 
• Deposited Residue Count: 1,404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WbgU	A, B, C [auth S], D [auth b]	351	Plesiomonas shigelloides	Mutation(s): 0  Gene Names: wbgU EC: 5.1.3.7
UniProt
Find proteins for Q7BJX9 (Plesiomonas shigelloides) Explore Q7BJX9  Go to UniProtKB:  Q7BJX9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], H [auth B], J [auth S], L [auth b]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
UDP	F [auth A], I [auth B], K [auth S], M [auth b]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.978	α = 90
b = 77.978	β = 90
c = 223.873	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Bhatt, V.S., Guan, W., Wang, P.G.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations