3VYO

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2 N140 truncation mutant (resideus 140-408)

• PDB DOI: https://doi.org/10.2210/pdb3VYO/pdb

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


• Deposited: 2012-09-30 Released: 2013-06-19 
• Deposition Author(s): Li, W.J., Li, D.F., Bi, L.J., Wang, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

Crystal structure of L,D-transpeptidase LdtMt2 in complex with meropenem reveals the mechanism of carbapenem against Mycobacterium tuberculosis

Li, W.J., Li, D.F., Hu, Y.L., Zhang, X.E., Bi, L.J., Wang, D.C.

(2013) Cell Res 23: 728-731

• PubMed: 23588382 
• DOI: https://doi.org/10.1038/cr.2013.53
• Primary Citation of Related Structures:  
  3VYN, 3VYO, 3VYP

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: 59.12 kDa 
• Atom Count: 4,519 
• Modelled Residue Count: 523 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable conserved lipoprotein LPPS	A, B	269	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: Rv2518c EC: 2.3.2.12
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2  Go to UniProtKB:  I6Y9J2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.37	α = 90
b = 121.19	β = 90
c = 122.99	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Li, W.J., Li, D.F., Bi, L.J., Wang, D.C.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release