9QUT | pdb_00009qut

Mycobacterium tuberculosis gyrase holocomplex with 150 bp DNA and corramycin

• PDB DOI: https://doi.org/10.2210/pdb9QUT/pdb
• EM Map EMD-53381: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis, Escherichia coli, Corallococcus coralloides
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-11 Released: 2026-10-21 
• Deposition Author(s): Petrella, S., Mechaly, A., Wormser, Y., Gubellini, F.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mycobacterium tuberculosis gyrase holocomplex with 150 bp DNA and corramycin

Petrella, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 521.31 kDa 
• Atom Count: 12,372 
• Modeled Residue Count: 1,496 
• Deposited Residue Count: 3,656 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B,DNA gyrase subunit A	A, B	1,518	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: gyrB, Rv0005, MTCY10H4.03, gyrA, Rv0006, MTCY10H4.04 EC: 5.6.2.2
UniProt
Find proteins for P9WG45 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG45  Go to UniProtKB:  P9WG45
Find proteins for P9WG47 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG47  Go to UniProtKB:  P9WG47
UniProt Groups	P9WG47P9WG45

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Corramycin	G, H	10	Corallococcus coralloides	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (150-mer)	C, E	150	Escherichia coli

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (150-mer)	D, F	150	Escherichia coli

Small Molecules

Modified Residues  4 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
OGC	G, H	DHI	Methylation	C7 H11 N3 O3
OGC	G, H	DHI	Hydroxylation	C7 H11 N3 O3
MEA	G, H	PHE	Methylation	C10 H13 N O2
HVA	G, H	VAL	Hydroxylation	C5 H11 N O3

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002426	G, H	Corramycin	Peptide-like / Antibiotic, Antimicrobial

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	Coot

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-21 
Deposition Author(s): Petrella, S., Mechaly, A., Wormser, Y., Gubellini, F.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR 24 CE92 0080 01 NAPGYR_0100000381

Revision History  

• Version 1.0: 2026-10-21
  Type: Initial release