6TAK

Crystal structure of Escherichia coli Orotate Phosphoribosyltransferase in complex with Orotic acid and Sulfate at 1.25 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6TAK/pdb

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

Deposited: 2019-10-29 Released: 2020-11-25
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.206
R-Value Work: 0.181
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

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

Macromolecule Content

Total Structure Weight: 48.92 kDa
Atom Count: 3,863
Modelled Residue Count: 420
Deposited Residue Count: 426
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A7E3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ORO (Subject of Investigation/LOI) Query on ORO Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain K [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain K [auth BBB]	C [auth AAA], K [auth BBB]	OROTIC ACID C₅ H₄ N₂ O₄ PXQPEWDEAKTCGB-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Focus chain K [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain K [auth BBB]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain J [auth BBB] SDF format, chain M [auth BBB] SDF format, chain N [auth BBB] SDF format, chain O [auth BBB] SDF format, chain P [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain J [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain O [auth BBB] MOL2 format, chain P [auth BBB]	E [auth AAA] F [auth AAA] G [auth AAA] H [auth AAA] J [auth BBB] E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], J [auth BBB], M [auth BBB], N [auth BBB], O [auth BBB], P [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain J [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain O [auth BBB] Focus chain P [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain J [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain O [auth BBB] Focus chain P [auth BBB]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain I [auth AAA] SDF format, chain L [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain R [auth BBB] SDF format, chain S [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain R [auth BBB] MOL2 format, chain S [auth BBB]	D [auth AAA] I [auth AAA] L [auth BBB] Q [auth BBB] R [auth BBB] D [auth AAA], I [auth AAA], L [auth BBB], Q [auth BBB], R [auth BBB], S [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.206
R-Value Work: 0.181
R-Value Observed: 0.182
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.658	α = 90
b = 69.469	β = 90
c = 104.383	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-25

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2020-11-25
Type: Initial release
Version 1.1: 2021-06-09
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

6TAK

Crystal structure of Escherichia coli Orotate Phosphoribosyltransferase in complex with Orotic acid and Sulfate at 1.25 Angstrom resolution

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)