5LHV | pdb_00005lhv

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine and sulfate ion at 1.29 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5LHV/pdb

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


• Deposited: 2016-07-13 Released: 2017-08-02 
• Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Balaev, V.V., Betzel, C., Mikhailov, A.M.
• Funding Organization(s): RFBR

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.178 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine and sulfate ion at 1.29 A resolution

Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., 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: 165.26 kDa 
• Atom Count: 13,501 
• Modeled Residue Count: 1,503 
• Deposited Residue Count: 1,506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E, F	251	Vibrio cholerae	Mutation(s): 0  Gene Names:  udp, udp_1, 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URI	DA [auth D], I [auth A], JA [auth E], Q [auth B], RA [auth F], W [auth C]	URIDINE C9 H12 N2 O6 DRTQHJPVMGBUCF-XVFCMESISA-N
URA	EA [auth D], J [auth A], KA [auth E], R [auth B], SA [auth F], X [auth C]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
SO4	CA [auth D], G [auth A], H [auth A], IA [auth E], O [auth B], P [auth B], QA [auth F], V [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	BA [auth C], HA [auth D], N [auth A], OA [auth E], U [auth B], VA [auth F], WA [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	GA [auth D], L [auth A], MA [auth E], T [auth B], UA [auth F], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	FA [auth D], K [auth A], LA [auth E], PA [auth E], S [auth B], TA [auth F], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	AA [auth C], M [auth A], NA [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.178 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.223	α = 69.7
b = 71.648	β = 72.7
c = 88.878	γ = 86.24

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: 2017-08-02 
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Balaev, V.V., Betzel, C., Mikhailov, A.M.

---

Funding Organization	Location	Grant Number
RFBR	Russian Federation	14-04-00952a

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description