7Q2W

Mutant T91S of uridine phosphorylase from Shewanella oneidensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Role of conformational changes of hexameric bacterial uridine phosphorylases in substrate binding

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

(2021) Crystallogr Rep 66: 786-790


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine phosphorylase251Shewanella oneidensis MR-1Mutation(s): 1 
Gene Names: udpSO_4133
EC: 2.4.2.3
UniProt
Find proteins for Q8E9X9 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8E9X9 
Go to UniProtKB:  Q8E9X9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8E9X9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
URA (Subject of Investigation/LOI)
Query on URA

Download Ideal Coordinates CCD File 
I [auth FFF]URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
G [auth DDD]
J [auth FFF]
K [auth FFF]
L [auth AAA]
N [auth EEE]
G [auth DDD],
J [auth FFF],
K [auth FFF],
L [auth AAA],
N [auth EEE],
O [auth BBB],
P [auth BBB]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
H [auth DDD],
M [auth AAA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.4α = 90
b = 95.49β = 120.025
c = 91.41γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedRussian Federation--

Revision History  (Full details and data files)

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