7Q1I | pdb_00007q1i

Hybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence glycerol

• PDB DOI: https://doi.org/10.2210/pdb7Q1I/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli MS 85-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-20 Released: 2022-04-06 
• Deposition Author(s): Polyakov, K., Safonova, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.229 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Hybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence glycerol

Polyakov, K., Safonova, T.

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.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 54.55 kDa 
• Atom Count: 4,152 
• Modeled Residue Count: 500 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A [auth AAA], B [auth BBB]	250	Escherichia coli MS 85-1	Mutation(s): 0  Gene Names: udp, HMPREF9350_04039 EC: 2.4.2.3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC (Subject of Investigation/LOI)	D [auth AAA], H [auth BBB]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
GOL	E [auth AAA], F [auth AAA], G [auth AAA], I [auth BBB]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K (Subject of Investigation/LOI)	C [auth AAA]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.229 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.179 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.52	α = 90
b = 150.52	β = 90
c = 46.25	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Polyakov, K., Safonova, T.

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Funding Organization	Location	Grant Number
Not funded	Russian Federation	--

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description