4OGL

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4OGL/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-16 Released: 2015-03-04 
• Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.115 (Depositor), 0.110 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Starting Model: experimental

Literature

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution

Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Balaev, T., Seregina, A.S., Mironov, C., Betzel, C., Mikhailov, A.M.

(2016) Crystallogr Rep 

• DOI: https://doi.org/10.1134/S1063774516060134

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)

Macromolecule Content

• Total Structure Weight: 164.71 kDa 
• Atom Count: 14,803 
• Modelled Residue Count: 1,502 
• 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 O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: Udp, VC_1034 EC: 2.4.2.3
UniProt
Find proteins for Q9KT71 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KT71  Go to UniProtKB:  Q9KT71

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TDR	BA [auth F], G [auth A], K [auth B], N [auth C], T [auth D], W [auth E]	THYMINE C5 H6 N2 O2 RWQNBRDOKXIBIV-UHFFFAOYSA-N
TRS	M [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	EA [auth F], I [auth A], R [auth C], U [auth D], V [auth D], Z [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	CA [auth F], DA [auth F], H [auth A], L [auth B], O [auth C], P [auth C], Q [auth C], X [auth E], Y [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	AA [auth E], J [auth A], S [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.115 (Depositor), 0.110 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.748	α = 90
b = 96.499	β = 119.99
c = 92.776	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2017-01-11
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description