5LOK | pdb_00005lok

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.11 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5LOK/pdb

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


• Deposited: 2016-08-09 Released: 2017-08-23 
• Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Dontsova, M.V., Betzel, C., Mikhailov, A.M.
• Funding Organization(s): RFBR, Grant of President of Russian Federation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 
  0.136 (Depositor), 0.137 (DCC) 
• R-Value Work: 
  0.114 (Depositor), 0.116 (DCC) 
• R-Value Observed: 
  0.115 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.11 A resolution

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

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)

Macromolecule Content 

• Total Structure Weight: 166.06 kDa 
• Atom Count: 14,450 
• Modeled Residue Count: 1,509 
• 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, DN30_1909 EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae) Explore Q9K4U1  Go to UniProtKB:  Q9K4U1

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTN	FA [auth E], I [auth A], JA [auth F], P [auth B], U [auth C], Y [auth D]	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C9 H13 N3 O5 UHDGCWIWMRVCDJ-XVFCMESISA-N
CYT	GA [auth E], J [auth A], KA [auth F], Q [auth B], V [auth C], X [auth D], Z [auth D]	6-AMINOPYRIMIDIN-2(1H)-ONE C4 H5 N3 O OPTASPLRGRRNAP-UHFFFAOYSA-N
SO4	L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth D], HA [auth E], K [auth A], LA [auth F], R [auth B], W [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	DA [auth E], G [auth A], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	EA [auth E], H [auth A], T [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	BA [auth E], CA [auth E], IA [auth F], M [auth B], N [auth B], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free:  0.136 (Depositor), 0.137 (DCC) 
• R-Value Work:  0.114 (Depositor), 0.116 (DCC) 
• R-Value Observed: 0.115 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.258	α = 69.35
b = 71.772	β = 72.17
c = 89.228	γ = 85.78

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-08-23 
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Dontsova, M.V., Betzel, C., Mikhailov, A.M.

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Funding Organization	Location	Grant Number
RFBR	Russian Federation	14-04-00952a
Grant of President of Russian Federation	Russian Federation	MK-9246.2016.3

Revision History  

• Version 1.0: 2017-08-23
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description