7R8Z | pdb_00007r8z

Ancestral protein AncEn of Phosphomethylpyrimidine kinases family

• PDB DOI: https://doi.org/10.2210/pdb7R8Z/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., Fuentes-Ugarte, N., 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: 2.30 Å
• R-Value Free: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.14 kDa 
• Atom Count: 1,711 
• Modeled Residue Count: 222 
• Deposited Residue Count: 287 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAR	B [auth A], C [auth A]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N
BME	D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.451	α = 90
b = 78.451	β = 90
c = 142.973	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., Fuentes-Ugarte, N., 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 2.0: 2023-11-15
  Type: Coordinate replacement
  Reason: Atomic clashes
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Structure summary
• Version 2.1: 2024-08-21
  Changes: Database references