8SLG

Crystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (glycyl adenylate bound)

• PDB DOI: https://doi.org/10.2210/pdb8SLG/pdb

• Classification: LIGASE
• Organism(s): Mycolicibacterium thermoresistibile ATCC 19527
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-04-21 Released: 2023-05-03 
• 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: 1.95 Å
• R-Value Free: 0.201 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Crystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (glycyl adenylate bound)

Liu, L., Lovell, S., Battaile, K.P., Seibold, S.

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: 111.42 kDa 
• Atom Count: 7,437 
• Modelled Residue Count: 876 
• Deposited Residue Count: 964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine--tRNA ligase	A, B	482	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 0  Gene Names: glyQS EC: 6.1.1.14
UniProt
Find proteins for G7CIG9 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CIG9  Go to UniProtKB:  G7CIG9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G5A (Subject of Investigation/LOI)	C [auth A], I [auth B]	5'-O-(glycylsulfamoyl)adenosine C12 H17 N7 O7 S AMWPZASLDLLQFT-JJNLEZRASA-N
GOL	F [auth B], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.201 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M38SLG

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.248	α = 90
b = 87.108	β = 104.21
c = 99.358	γ = 90

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: 2023-05-03 
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	HHSN272201700059C
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary