6TAJ

Crystal structure of Escherichia coli Orotate Phosphoribosyltransferase in complex with Orotic acid 1.60 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6TAJ/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-29 Released: 2020-11-18 
• Deposition Author(s): Navas-Yuste, S., Lopez-Estepa, M., Gomez, S., Fernandez, F.J., Vega, M.C.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness, Spanish Ministry of Science, Innovation, and Universities, Spanish National Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.223 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by Means of X-ray Crystallography and Computational Simulations

Roca, M., Navas-Yuste, S., Zinovjev, K., Lopez-Estepa, M., Gomez, S., Fernandez, F.J., Vega, M.C., Tunon, I.

(2020) ACS Catal 10: 1871-1885

• DOI: https://doi.org/10.1021/acscatal.9b05294

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47.69 kDa 
• Atom Count: 3,494 
• Modelled Residue Count: 409 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotate phosphoribosyltransferase	A [auth AAA], B [auth BBB]	213	Escherichia coli K-12	Mutation(s): 0  Gene Names: pyrE, b3642, JW3617 EC: 2.4.2.10
UniProt
Find proteins for P0A7E3 (Escherichia coli (strain K12)) Explore P0A7E3  Go to UniProtKB:  P0A7E3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ORO (Subject of Investigation/LOI)	C [auth AAA], E [auth BBB]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
GOL	D [auth AAA], F [auth BBB]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.223 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.118	α = 90
b = 83.118	β = 90
c = 122.787	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Navas-Yuste, S., Lopez-Estepa, M., Gomez, S., Fernandez, F.J., Vega, M.C.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2015-66206-C2-2-R
Spanish Ministry of Science, Innovation, and Universities	Spain	RTI2018-1018-102242-B-I00
Spanish National Research Council	Spain	2016E064

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 2.0: 2021-05-26
  Changes: Atomic model
• Version 2.1: 2021-06-02
  Changes: Database references
• Version 2.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description