6Y8L

Mycobacterium thermoresistibile GyrB21 in complex with novobiocin

• PDB DOI: https://doi.org/10.2210/pdb6Y8L/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycolicibacterium thermoresistibile
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-03-05 Released: 2020-08-12 
• Deposition Author(s): Henderson, S.R., Stevenson, C.E.M., Malone, B., Zholnerovych, Y., Mitchenall, L.A., Pichowicz, M., McGarry, D.H., Cooper, I.R., Charrier, C., Salisbury, A., Lawson, D.M., Maxwell, A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.181 
• R-Value Work: 0.140 
• R-Value Observed: 0.142 

Literature

Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase.

Henderson, S.R., Stevenson, C.E.M., Malone, B., Zholnerovych, Y., Mitchenall, L.A., Pichowicz, M., McGarry, D.H., Cooper, I.R., Charrier, C., Salisbury, A.M., Lawson, D.M., Maxwell, A.

(2020) J Antimicrob Chemother 75: 2835-2842

• PubMed: 32728686 
• DOI: https://doi.org/10.1093/jac/dkaa286
• Primary Citation of Related Structures:  
  6Y8L, 6Y8N, 6Y8O


• PubMed Abstract: 
  

  To evaluate the efficacy of two novel compounds against mycobacteria and determine the molecular basis of their action on DNA gyrase using structural and mechanistic approaches.

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Organizational Affiliation: 

Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.4 kDa 
• Atom Count: 3,305 
• Modelled Residue Count: 363 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A, B	186	Mycolicibacterium thermoresistibile	Mutation(s): 2  Gene Names: gyrB, RMCT_1109 EC: 5.6.2.2
UniProt
Find proteins for G7CIP8 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CIP8  Go to UniProtKB:  G7CIP8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NOV (Subject of Investigation/LOI)	C [auth A], J [auth B]	NOVOBIOCIN C31 H36 N2 O11 YJQPYGGHQPGBLI-KGSXXDOSSA-N
ZN	D [auth A], E [auth A], F [auth A], I [auth A], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.181 
• R-Value Work: 0.140 
• R-Value Observed: 0.142 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.962	α = 90
b = 51.114	β = 100.32
c = 83.205	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Henderson, S.R., Stevenson, C.E.M., Malone, B., Zholnerovych, Y., Mitchenall, L.A., Pichowicz, M., McGarry, D.H., Cooper, I.R., Charrier, C., Salisbury, A., Lawson, D.M., Maxwell, A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P012523/1
Wellcome Trust	United Kingdom	110072/Z/15/Z

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2020-09-30
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description