9FZ6

A 2.58A crystal structure of S. aureus DNA gyrase and DNA with metals identified through anomalous scattering

• PDB DOI: https://doi.org/10.2210/pdb9FZ6/pdb

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus, DNA molecule
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-07-04 Released: 2024-10-23 
• Deposition Author(s): Morgan, H., Duman, R., Bax, B.D., Warren, A.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.200 
• R-Value Work: 0.140 
• R-Value Observed: 0.152 

Starting Model: experimental

Literature

How do gepotidacin and zolifodacin stabilize DNA-cleavage complexes with bacterial type IIA topoisomerases? 1. Experimental definition of metal binding sites

Morgan, H., Nicholls, R., Warren, A.J., Ward, S., Evans, G., Long, F., Murshudov, G., Duman, R., Bax, B.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 166.76 kDa 
• Atom Count: 11,963 
• Modelled Residue Count: 1,383 
• Deposited Residue Count: 1,390 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	A, C	483	Staphylococcus aureus	Mutation(s): 1  Gene Names: gyrA EC: 5.6.2.2
UniProt
Find proteins for P20831 (Staphylococcus aureus) Explore P20831  Go to UniProtKB:  P20831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	B, D	190	Staphylococcus aureus	Mutation(s): 0  Gene Names: gyrB EC: 5.6.2.2
UniProt
Find proteins for P0A0K8 (Staphylococcus aureus) Explore P0A0K8  Go to UniProtKB:  P0A0K8

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')	E, F	8	DNA molecule

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')	G, H	14	DNA molecule

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB (Subject of Investigation/LOI)	M [auth C]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
GOL	I [auth A], J [auth A], N [auth C], O [auth C], P [auth C], Q [auth C], S [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	K [auth B], L [auth C], R [auth D], T [auth G], U [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.200 
• R-Value Work: 0.140 
• R-Value Observed: 0.152 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.633	α = 90
b = 93.633	β = 90
c = 410.874	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Morgan, H., Duman, R., Bax, B.D., Warren, A.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release