5XUO

Pks13 AT domain fragment from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb5XUO/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli DH1
• Mutation(s): No 


• Deposited: 2017-06-24 Released: 2018-05-02 
• Deposition Author(s): Yu, M.J., Gu, Y.J., Dou, C., Cheng, W.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.261 
• R-Value Work: 0.237 
• R-Value Observed: 0.238 

Literature

Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain fromMycobacterium tuberculosis

Yu, M., Dou, C., Gu, Y., Cheng, W.

(2018) PeerJ 6: e4728-e4728

• PubMed: 29761048 
• DOI: https://doi.org/10.7717/peerj.4728
• Primary Citation of Related Structures:  
  5XUO


• PubMed Abstract: 
  

  Type I polyketide synthase 13 (Pks13) is involved in the final step of the biosynthesis of mycolic acid in Mycobacterium tuberculosis . Recent articles have reported that Pks13 is an essential enzyme in the mycolic acid biosynthesis pathway, and it has been deeply studied as a drug target in Tuberculosis. We report a high-resolution structure of the acyltransferase (AT) domain of Pks13 at 2.59 Å resolution. Structural comparison with the full-length AT domain (PDB code, 3TZW, and 3TZZ) reveals a different orientation of the C-terminal helix and rearrangement of some conserved residues.

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Organizational Affiliation: 

Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.95 kDa 
• Atom Count: 841 
• Modelled Residue Count: 111 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase Pks13	A	111	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: pks13, Rv3800c
UniProt
Find proteins for I6X8D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6X8D2  Go to UniProtKB:  I6X8D2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.261 
• R-Value Work: 0.237 
• R-Value Observed: 0.238 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.443	α = 90
b = 94.443	β = 90
c = 96.975	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Yu, M.J., Gu, Y.J., Dou, C., Cheng, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	00402354011009

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2018-05-30
  Changes: Data collection, Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references