8REQ

Crystal structure of reduced ThyX-Y91F mutant

PDB DOI: https://doi.org/10.2210/pdb8REQ/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: 1.94 Å
R-Value Free: 0.240
R-Value Work: 0.213
R-Value Observed: 0.214

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: 115.78 kDa
Atom Count: 7,686
Modelled Residue Count: 871
Deposited Residue Count: 928
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDA (Subject of Investigation/LOI) Query on FDA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	H [auth A], N [auth B], Q [auth C], V [auth D]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C₂₇ H₃₅ N₉ O₁₅ P₂ YPZRHBJKEMOYQH-UYBVJOGSSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D]
PG6 Query on PG6 Download Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain P [auth C] mmCIF format, chain E [auth A] mmCIF format, chain P [auth C]	E [auth A], P [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain P [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain T [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain T [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain T [auth D]	BA [auth D], F [auth A], L [auth B], M [auth B], T [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth D] Interactions & Density Focus chain BA [auth D] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] G [auth A] I [auth A] J [auth A] K [auth A] AA [auth D], G [auth A], I [auth A], J [auth A], K [auth A], R [auth C], S [auth C], U [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.240
R-Value Work: 0.213
R-Value Observed: 0.214
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.02	α = 90
b = 117.09	β = 90
c = 141.967	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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