5MIW | pdb_00005miw

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uracil at 1.28 A.

• PDB DOI: https://doi.org/10.2210/pdb5MIW/pdb

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


• Deposited: 2016-11-29 Released: 2017-12-20 
• Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.169 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uracil at 1.28 A.

Prokofev, I.I., Lashkov, A.A., Balaev, V.V., 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: 164.99 kDa 
• Atom Count: 14,909 
• 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 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	DA [auth D], IA [auth E], J [auth A], LA [auth F], O [auth B], W [auth C]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
SO4	K [auth A], P [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	EA [auth D], FA [auth D], JA [auth E], L [auth A], MA [auth F], NA [auth F], Q [auth B], R [auth B], X [auth C], Y [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	N [auth B], V [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	AA [auth D], BA [auth D], G [auth A], GA [auth E], KA [auth F], M [auth B], T [auth C], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	CA [auth D], H [auth A], HA [auth E], I [auth A], S [auth B], Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free:  0.169 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.513	α = 69.22
b = 71.948	β = 72.2
c = 89.332	γ = 85.6

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description