8PXY

Crystal structure of the transpeptidase LdtMt2 C354S mutant from Mycobacterium tuberculosis in complex with natural substrate

• PDB DOI: https://doi.org/10.2210/pdb8PXY/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-07-24 Released: 2024-08-07 
• Deposition Author(s): de Munnik, M., Schofield, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.246 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Crystal structure of the transpeptidase LdtMt2 C354S mutant from Mycobacterium tuberculosis in complex with natural substrate

de Munnik, M., Schofield, C.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 39.22 kDa 
• Atom Count: 3,073 
• Modelled Residue Count: 354 
• Deposited Residue Count: 359 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase 2	A	355	Mycobacterium tuberculosis	Mutation(s): 1  Gene Names: ldtB, MT2594, V735_02606 EC: 2.3.2
UniProt
Find proteins for O53223 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)) Explore O53223  Go to UniProtKB:  O53223

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan tetrapeptide	B	4	Mycobacterium tuberculosis	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid	C	2		N/A
Glycosylation Resources
GlyTouCan:  G88499BX GlyCosmos:  G88499BX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.246 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.608	α = 90
b = 94.623	β = 90
c = 58.794	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): de Munnik, M., Schofield, C.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release