8U2Q | pdb_00008u2q

Crystal Structure of Glycine--tRNA ligase active site chimera from Mycobacterium thermoresistibile/tuberculosis (G5A bound)

PDB DOI: https://doi.org/10.2210/pdb8U2Q/pdb

Classification: TRANSFERASE
Organism(s): Mycolicibacterium thermoresistibile ATCC 19527
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Glycine--tRNA ligase active site chimera from Mycobacterium thermoresistibile/tuberculosis (G5A bound)

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

To be published.

Macromolecule Content

Total Structure Weight: 110.38 kDa
Atom Count: 6,829
Modeled Residue Count: 834
Deposited Residue Count: 958
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine--tRNA ligase	A, B	479	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 3 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G7CIG9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G5A (Subject of Investigation/LOI) Query on G5A Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	5'-O-(glycylsulfamoyl)adenosine C₁₂ H₁₇ N₇ O₇ S AMWPZASLDLLQFT-JJNLEZRASA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.186 (Depositor)

Diffraction Data: https://doi.org/10.18430/m38u2q

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.286	α = 90
b = 87.388	β = 104.12
c = 99.152	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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)

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