4OGL

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution

Prokofev, I.I.Lashkov, A.A.Gabdoulkhakov, A.G.Balaev, T.Seregina, A.S.Mironov, C.Betzel, C.Mikhailov, A.M.

(2016) Crystallogr Rep 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine phosphorylase
A, B, C, D, E
A, B, C, D, E, F
253Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: UdpVC_1034
EC: 2.4.2.3
UniProt
Find proteins for Q9KT71 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KT71 
Go to UniProtKB:  Q9KT71
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KT71
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TDR
Query on TDR

Download Ideal Coordinates CCD File 
BA [auth F]
G [auth A]
K [auth B]
N [auth C]
T [auth D]
BA [auth F],
G [auth A],
K [auth B],
N [auth C],
T [auth D],
W [auth E]
THYMINE
C5 H6 N2 O2
RWQNBRDOKXIBIV-UHFFFAOYSA-N
TRS
Query on TRS

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M [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

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EA [auth F]
I [auth A]
R [auth C]
U [auth D]
V [auth D]
EA [auth F],
I [auth A],
R [auth C],
U [auth D],
V [auth D],
Z [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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CA [auth F]
DA [auth F]
H [auth A]
L [auth B]
O [auth C]
CA [auth F],
DA [auth F],
H [auth A],
L [auth B],
O [auth C],
P [auth C],
Q [auth C],
X [auth E],
Y [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth E],
J [auth A],
S [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.748α = 90
b = 96.499β = 119.99
c = 92.776γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description