7R8Y | pdb_00007r8y

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.254 (Depositor), 0.258 (DCC)
R-Value Work:
0.232 (Depositor), 0.234 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7R8Y

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

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

Macromolecule Content

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

Macromolecules

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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	3D Interactions
HMH Query on HMH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE C₆ H₉ N₃ O VUTBELPREDJDDH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.254 (Depositor), 0.258 (DCC)
R-Value Work: 0.232 (Depositor), 0.234 (DCC)
R-Value Observed: 0.233 (Depositor)

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-29

Deposition Author(s):

Gonzalez-Ordenes, F.

Castro-Fernandez, V.

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.