8REP

Crystal structure of oxidized ThyX-Y91F mutant

PDB DOI: https://doi.org/10.2210/pdb8REP/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-12-12 Released: 2025-01-01
Deposition Author(s): Pecqueur, L., Hamdane, D.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.241
R-Value Work: 0.222
R-Value Observed: 0.223

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural Plasticity of Flavin-dependent Thymidylate Synthase controlled by the enzyme redox state

Pecqueur, L., Lombard, M., Hamdane, D.

To be published.

Macromolecule Content

Total Structure Weight: 114.59 kDa
Atom Count: 7,398
Modelled Residue Count: 857
Deposited Residue Count: 928
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin-dependent thymidylate synthase	A, B, C, D	232	Thermotoga maritima	Mutation(s): 1 Gene Names: thyX EC: 2.1.1.148
UniProt
Find proteins for Q9WYT0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYT0 Go to UniProtKB: Q9WYT0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WYT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D]	H [auth A], J [auth B], L [auth C], Q [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain Q [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C]	E [auth A], F [auth A], K [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain O [auth D] SDF format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D] MOL2 format, chain M [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth D] mmCIF format, chain M [auth D]	G [auth A], I [auth B], M [auth D], O [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth D] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth D] Focus chain O [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain P [auth D] SDF format, chain R [auth D] MOL2 format, chain N [auth D] MOL2 format, chain P [auth D] MOL2 format, chain R [auth D] mmCIF format, chain N [auth D] mmCIF format, chain P [auth D] mmCIF format, chain R [auth D]	N [auth D], P [auth D], R [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Focus chain P [auth D] Focus chain R [auth D] Interactions & Density Focus chain N [auth D] Focus chain P [auth D] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.241
R-Value Work: 0.222
R-Value Observed: 0.223
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.919	α = 90
b = 116.801	β = 90
c = 142.754	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
TRUNCATE	data processing
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-01

Deposition Author(s):

Pecqueur, L.

Hamdane, D.

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-15-CE11-0004-01
Agence Nationale de la Recherche (ANR)	France	ANR-11-LABX-0011-01
Agence Nationale de la Recherche (ANR)	France	ANR-11-IDEX-0004-02