6EYP

X-ray structure of the unliganded uridine phosphorylase from Vibrio cholerae at 1.22A

• PDB DOI: https://doi.org/10.2210/pdb6EYP/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-13 Released: 2018-11-21 
• Deposition Author(s): Prokofev, I.I., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Lashkov, A.A.
• Funding Organization(s): Grant of the President of Russian Federation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 0.170 
• R-Value Work: 0.138 
• R-Value Observed: 0.138 

Literature

X-ray structure of the unliganded uridine phosphorylase from Vibrio cholerae at 1.22A

Prokofev, I.I., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Lashkov, A.A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 163.48 kDa 
• Atom Count: 14,636 
• Modelled Residue Count: 1,508 
• Deposited Residue Count: 1,518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E, F	253	Vibrio cholerae	Mutation(s): 0  Gene Names:  udp, udp_1, B2J67_05455, B2J68_05210, B2J71_05165, BFX32_04820, BTY66_05555, CEF09_03900, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377 EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae) Explore Q9K4U1  Go to UniProtKB:  Q9K4U1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], I [auth B], J [auth C], M [auth D], N [auth D], O [auth E], Q [auth F], R [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	H [auth A], K [auth C], P [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 0.170 
• R-Value Work: 0.138 
• R-Value Observed: 0.138 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.94	α = 90
b = 92.94	β = 90
c = 140.231	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Prokofev, I.I., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Lashkov, A.A.

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Funding Organization	Location	Grant Number
Grant of the President of Russian Federation	Russian Federation	MK-9246.2016.3.

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description