6LQB | pdb_00006lqb

A third intermediate state of L,D-transpeptidase LdtMt2-ertapenem adduct

• PDB DOI: https://doi.org/10.2210/pdb6LQB/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-13 Released: 2021-01-13 
• Deposition Author(s): Li, D.F., Qin, Y.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

A New State I-plus Observed for the L,D-transpeptidase LdtMt2-ertapenem Adduct

Wang, X.Y., Qin, Y.L., Han, Q., Gu, X.E., Yan, Z., Fu, K., Li, D.F., Deng, K.

(2020) PROG BIOCHEM BIOPHYS 47: 989-997

• DOI: https://doi.org/10.16476/j.pibb.2020.0079

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: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.94 kDa 
• Atom Count: 4,578 
• Modeled Residue Count: 531 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase 2	A, B	269	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 EC: 2.3.2
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2  Go to UniProtKB:  I6Y9J2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2RG (Subject of Investigation/LOI)	C [auth A], G [auth B]	(2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C22 H27 N3 O7 S RALHTEQYPKBGFO-SAGZMZRGSA-N
GOL	D [auth A], E [auth A], F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	I [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.181	α = 90
b = 73.207	β = 90
c = 103.803	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Li, D.F., Qin, Y.L.

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-07-28
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary