4OEH | pdb_00004oeh

X-ray Structure of Uridine Phosphorylase from Vibrio cholerae Complexed with Uracil at 1.91 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb4OEH/pdb

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


• Deposited: 2014-01-13 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: 1.91 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases.

Prokofev, I.I., Lashkov, A.A., Balaev, T., Seregina, A.S., Mironov, C., Gabdoulkhakov, A.G., 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: 164.31 kDa 
• Atom Count: 12,849 
• Modeled Residue Count: 1,506 
• 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 Q9K4U1 (Vibrio cholerae) Explore Q9K4U1  Go to UniProtKB:  Q9K4U1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URA	G [auth A], K [auth B], U [auth E], X [auth F]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
PEG	M [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth A], L [auth B], O [auth C], R [auth D], V [auth E], Y [auth F], Z [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	I [auth A], P [auth C], Q [auth C], W [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
EOH	AA [auth F], J [auth A], S [auth D]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
NA	BA [auth F], N [auth B], T [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.255	α = 69.14
b = 71.763	β = 72.15
c = 89.321	γ = 85.79

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XSCALE	data scaling

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: 2015-03-11
  Changes: Other
• Version 1.2: 2017-01-11
  Changes: Database references
• Version 1.3: 2018-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2018-03-07
  Changes: Data collection
• Version 1.5: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description