6Z9Z

Atomic resolution X-ray structure of the Uridine phosphorylase from Vibrio cholerae on crystals grown under microgravity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.126 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystallization in Microgravity and the Atomic-Resolution Structure of Uridine Phosphorylase from Vibrio cholerae

Eistrikh-Heller, P.A.Rubinsky, S.V.Samygina, V.R.Gabdulkhakov, A.G.Kovalchuk, M.V.Mironov, A.S.Lashkov, A.A.

(2021) Crystallogr Rep 66: 777-785


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 choleraeMutation(s): 0 
Gene Names: 
EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae)
Explore Q9K4U1 
Go to UniProtKB:  Q9K4U1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K4U1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CA [auth D],
W [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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EA [auth E],
G [auth A],
L [auth B],
S [auth C],
X [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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DA [auth E]
FA [auth E]
H [auth A]
I [auth A]
KA [auth F]
DA [auth E],
FA [auth E],
H [auth A],
I [auth A],
KA [auth F],
LA [auth F],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
Y [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

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BA [auth D],
IA [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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AA [auth D]
GA [auth E]
HA [auth E]
J [auth A]
JA [auth E]
AA [auth D],
GA [auth E],
HA [auth E],
J [auth A],
JA [auth E],
K [auth A],
P [auth B],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.126 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.186α = 90
b = 97.061β = 119.965
c = 93.227γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation19-29-12054
Ministry of Education and Science of the Russian FederationRussian Federation0026-2019-0002

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-04-10
    Changes: Database references