3QJ7

Crystal Structure of the Mycobacterium tuberculosis Thymidylate synthase (ThyA) bound to dUMP

• PDB DOI: https://doi.org/10.2210/pdb3QJ7/pdb

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


• Deposited: 2011-01-28 Released: 2011-06-15 
• 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: 2.50 Å
• R-Value Free: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.167 (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., Harshbarger, W., 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: 121.32 kDa 
• Atom Count: 8,990 
• Modelled Residue Count: 1,037 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B, C, D	264	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: MT2834, MTV002.29c, 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
UMP	E [auth A], G [auth B], H [auth C], I [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
SPM	F [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.956	α = 90
b = 84.85	β = 131.21
c = 130.065	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
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: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description