8U2P

Crystal Structure of Glycine--tRNA ligase from Mycobacterium tuberculosis (G5A bound)

• PDB DOI: https://doi.org/10.2210/pdb8U2P/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 


• Deposited: 2023-09-06 Released: 2023-09-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.208 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Crystal Structure of Glycine--tRNA ligase from Mycobacterium tuberculosis (G5A bound)

Seibold, S., Lovell, S., Battaile, K.P., DeRocher, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 55.49 kDa 
• Atom Count: 3,405 
• Modelled Residue Count: 401 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine--tRNA ligase	A	476	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: glyQS, glyS, Rv2357c, MTCY27.23, MTCY98.26 EC: 6.1.1.14
UniProt
Find proteins for P9WFV7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFV7  Go to UniProtKB:  P9WFV7

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G5A (Subject of Investigation/LOI)	B [auth A]	5'-O-(glycylsulfamoyl)adenosine C12 H17 N7 O7 S AMWPZASLDLLQFT-JJNLEZRASA-N
MES	E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
IMD	C [auth A], D [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.208 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 6₁ 2 2
• Diffraction Data: https://doi.org/10.18430/m38u2p

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.293	α = 90
b = 124.293	β = 90
c = 131.383	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release
  
• Version 1.1: 2024-04-10
  Changes: Source and taxonomy