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
NAKB: 9FZ6

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

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

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

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20831
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A0K8
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(APGPCPCPGPTPAPG)-3')	E, F	8	DNA molecule
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(APGPTPAPCPCPTPAPCPGPGPCP*T)-3')	G, H	14	DNA molecule
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB (Subject of Investigation/LOI) Query on BTB Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth E]	I [auth A] J [auth A] N [auth C] O [auth C] P [auth C] 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		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth E] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth E]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain R [auth D] SDF format, chain T [auth G] SDF format, chain U [auth H] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth G] MOL2 format, chain U [auth H] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth G] mmCIF format, chain U [auth H]	K [auth B], L [auth C], R [auth D], T [auth G], U [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth C] Focus chain R [auth D] Focus chain T [auth G] Focus chain U [auth H] Interactions & Density Focus chain K [auth B] Focus chain L [auth C] Focus chain R [auth D] Focus chain T [auth G] Focus chain U [auth H]