5JFE

Flavin-dependent thymidylate synthase with H2-dUMP

• PDB DOI: https://doi.org/10.2210/pdb5JFE/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-04-19 Released: 2017-04-26 
• Deposition Author(s): Sapra, A., Stuckey, J., Palfey, B.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.190 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Evaluating H2-dUMP as an Intermediate in the oxidation of Flavin-dependent Thymidylate Synthase

Sapra, A., Stuckey, J., Palfey, B.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.91 kDa 
• Atom Count: 2,103 
• Modelled Residue Count: 213 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase ThyX	A	232	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: thyX, thy1, TM_0449 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
UMC	C [auth A]	2'-deoxy-5'-uridylic acid C9 H15 N2 O8 P WQQZADPPRABIFU-SHYZEUOFSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.190 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.322	α = 90
b = 110.322	β = 90
c = 120.765	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
HKL-2000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Sapra, A., Stuckey, J., Palfey, B.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	NSF CHE 1213620

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description