4QR7

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

• PDB DOI: https://doi.org/10.2210/pdb4QR7/pdb

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


• Deposited: 2014-06-30 Released: 2015-07-29 
• Deposition Author(s): Gokulan, K., Varughese, K.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.268 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Literature

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

Gokulan, K., Khare, S., Cerniglia, C.E., Foley, S.L., Varughese, K.I.

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.99 kDa 
• Atom Count: 2,794 
• Modelled Residue Count: 349 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,d-transpeptidase LdtB	A	352	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: ldtB, Rv2518c, RVBD_2518c EC: 2.3.2
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2  Go to UniProtKB:  I6Y9J2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLD	B [auth A]	GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA C37 H59 N7 O20 UPFMKPIBAIPLHT-RSJSDIDPSA-N
DWZ	C [auth A]	(2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C17 H27 N3 O5 S UUIYVKJXUXGPKB-VGWSNGFZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.268 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.33	α = 90
b = 66.459	β = 90
c = 206.865	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
Auto-Rickshaw	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Gokulan, K., Varughese, K.I.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2016-08-24
  Changes: Structure summary
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2022-02-02
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Structure summary