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.

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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/cr.2013.53
Primary Citation of Related Structures:
3VYN, 3VYO, 3VYP

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 (PDB Primary Data), 2.3.2 (UniProt)
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2 Go to UniProtKB: I6Y9J2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6Y9J2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-06-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-19
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.