7Q32 | pdb_00007q32

Mutant D24G of uridine phosphorylase from E. coli

• PDB DOI: https://doi.org/10.2210/pdb7Q32/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-10-26 Released: 2022-05-04 
• Deposition Author(s): Safonova, T., Polyakov, K., Antipov, A., Okorokova, N., Mordkovich, N., Veiko, V.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.160 (DCC) 

Starting Model: experimental

Literature

Mutant D24G of uridine phosphorylase from E. coli

Polyakov, K., Safonova, T., Antipov, A., Okorokova, N., Mordkovich, N., Veiko, V.

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)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 53.98 kDa 
• Atom Count: 4,166 
• 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 K-12	Mutation(s): 1  Gene Names: udp, b3831, JW3808 EC: 2.4.2.3
UniProt
Find proteins for P12758 (Escherichia coli (strain K12)) Explore P12758  Go to UniProtKB:  P12758

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC (Subject of Investigation/LOI)	C [auth AAA], E [auth BBB]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
K (Subject of Investigation/LOI)	D [auth BBB]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.160 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.07	α = 90
b = 150.07	β = 90
c = 46.36	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: 2022-05-04 
Deposition Author(s): Safonova, T., Polyakov, K., Antipov, A., Okorokova, N., Mordkovich, N., Veiko, V.

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Funding Organization	Location	Grant Number
Not funded	Russian Federation	--

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Database references, Structure summary
• Version 1.2: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description