3U1Q

Crystal Structure of M. tuberculosis LD-transpeptidase type 2 with 2-Mercaptoethanol

• PDB DOI: https://doi.org/10.2210/pdb3U1Q/pdb

• Classification: PEPTIDOGLYCAN BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-30 Released: 2012-12-05 
• Deposition Author(s): Erdemli, S., Bianchet, M.A., Gupta, R., Lamichhane, G., Amzel, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.244 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Literature

The Structure of Mycobacterium tuberculosis L,D-transpeptidase 2 provides insights into targeting the cell wall of persisters

Erdemli, S.B., Gupta, R., Lamichhane, G., Bishai, W., Amzel, L.M., Bianchet, M.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.2 kDa 
• Atom Count: 4,327 
• Modelled Residue Count: 520 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycobacteria Tuberculosis LD-transpeptidase type 2	A, B	287	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: lppS, MT2594, Rv2518c EC: 2.3.2
UniProt
Find proteins for O53223 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)) Explore O53223  Go to UniProtKB:  O53223

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
BME	C [auth A], D [auth A], G [auth B], H [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.244 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.689	α = 90
b = 121.013	β = 90
c = 122.799	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Erdemli, S., Bianchet, M.A., Gupta, R., Lamichhane, G., Amzel, L.M.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations