6Z9Z | pdb_00006z9z

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

• PDB DOI: https://doi.org/10.2210/pdb6Z9Z/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-04 Released: 2021-06-30 
• Deposition Author(s): Eistrikh-Heller, P.A., Rubinsky, S.V., Samygina, V.R., Gabdulkhakov, A.G., Lashkov, A.A.
• Funding Organization(s): Russian Foundation for Basic Research, Ministry of Education and Science of the Russian Federation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 
  0.142 (Depositor), 0.141 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.125 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

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

• DOI: https://doi.org/10.1134/S1063774521050059

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: 164.37 kDa 
• Atom Count: 14,294 
• Modeled Residue Count: 1,499 
• Deposited Residue Count: 1,518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E, F	253	Vibrio cholerae	Mutation(s): 0  Gene Names:  udp, udp_1, BC353_05040, C9J66_05900, D2927_05805, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377, FLM02_10845, FXF03_16695 EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae) Explore Q9K4U1  Go to UniProtKB:  Q9K4U1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	CA [auth D], W [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	EA [auth E], G [auth A], L [auth B], S [auth C], X [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	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	BA [auth D], IA [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	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 (Depositor), 0.141 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.125 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.186	α = 90
b = 97.061	β = 119.965
c = 93.227	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Eistrikh-Heller, P.A., Rubinsky, S.V., Samygina, V.R., Gabdulkhakov, A.G., Lashkov, A.A.

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Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	19-29-12054
Ministry of Education and Science of the Russian Federation	Russian Federation	0026-2019-0002

Revision History  

• 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