7R8Y

Ancestral protein AncThEn of Phosphomethylpyrimidine kinases family

• PDB DOI: https://doi.org/10.2210/pdb7R8Y/pdb

• Classification: TRANSFERASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-27 Released: 2022-06-29 
• Deposition Author(s): Munoz, S., Maturana, P., Gonzalez-Ordenes, F., Cea, P., Castro-Fernandez, V.
• Funding Organization(s): Comision Nacional Cientifica y Technologica (CONICYT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.232 
• R-Value Observed: 0.233 

Starting Model: experimental

Literature

Deciphering Structural Traits for Thermal and Kinetic Stability across Protein Family Evolution through Ancestral Sequence Reconstruction

Cea, P.A., Perez, M., Herrera, S.M., Munoz, S.M., Fuentes-Ugarte, N., Coche-Miranda, J., Maturana, P., Guixe, V., Castro-Fernandez, V.

(2024) Mol Biol Evol 41

• DOI: https://doi.org/10.1093/molbev/msae127

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.95 kDa 
• Atom Count: 3,109 
• Modelled Residue Count: 438 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphomethylpyrimidine Kinase	A, B	287	synthetic construct	Mutation(s): 0  EC: 2.7.4.7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HMH	C [auth A]	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE C6 H9 N3 O VUTBELPREDJDDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.232 
• R-Value Observed: 0.233 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.316	α = 90
b = 113.316	β = 90
c = 112.233	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Munoz, S., Maturana, P., Gonzalez-Ordenes, F., Cea, P., Castro-Fernandez, V.

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Funding Organization	Location	Grant Number
Comision Nacional Cientifica y Technologica (CONICYT)	Chile	1150460
Comision Nacional Cientifica y Technologica (CONICYT)	Chile	3160332
Comision Nacional Cientifica y Technologica (CONICYT)	Chile	EQM 120208

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-08-21
  Changes: Database references