8J65 | pdb_00008j65

the structure of L,D-transpeptidase LdtMt2 complex with citrate

• PDB DOI: https://doi.org/10.2210/pdb8J65/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-04-24 Released: 2024-05-01 
• Deposition Author(s): Li, D.F., Qin, Y.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Citrate interacts with L,D-transpeptidase and hinders the growth of Mycobacterium

Li, D.F., Qin, Y.L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.43 kDa 
• Atom Count: 4,335 
• Modeled Residue Count: 518 
• Deposited Residue Count: 586 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase 2	A, B	293	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: ldtB, MT2594, V735_02606 EC: 2.3.2
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2  Go to UniProtKB:  I6Y9J2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT (Subject of Investigation/LOI)	C [auth A], D [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.184	α = 90
b = 75.885	β = 111.92
c = 67.068	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Li, D.F., Qin, Y.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	92051101
National Natural Science Foundation of China (NSFC)	China	31870037

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release