4FOG | pdb_00004fog

Crystal Structure of Mtb ThyA in Complex with 5-Fluoro-dUMP and 5-methyltetrahydrofolic acid

• PDB DOI: https://doi.org/10.2210/pdb4FOG/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-20 Released: 2013-08-07 
• Deposition Author(s): Reddy, M.C.M., Bruning, J.B., Harshbarger, W., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.260 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of binary and ternary complexes of thymidylate synthase (ThyA) from Mycobacterium tuberculosis: Insights into the selectivity and mode of inhibition

Reddy, M.C.M., Bruning, J.B., Sacchettini, J.C.

To be published.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 122.22 kDa 
• Atom Count: 8,776 
• Modeled Residue Count: 1,043 
• Deposited Residue Count: 1,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B, C, D	263	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: MT2834, MTV002.29c, Rv2764c, thyA EC: 2.1.1.45
UniProt
Find proteins for P9WFR9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFR9  Go to UniProtKB:  P9WFR9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2F	F [auth A], I [auth C], K [auth D]	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID C20 H25 N7 O6 ZNOVTXRBGFNYRX-STQMWFEESA-N
UFP	E [auth A], G [auth B], H [auth C], J [auth D]	5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE C9 H12 F N2 O8 P HFEKDTCAMMOLQP-RRKCRQDMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.260 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.328	α = 90
b = 82.317	β = 132.3
c = 125.98	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Reddy, M.C.M., Bruning, J.B., Harshbarger, W., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description