9Y9Y | pdb_00009y9y

Crystal structure of DNA integrity scanning protein DisA from Mycobacterium tuberculosis in complex with cyclic di-AMP and bromide

PDB DOI: https://doi.org/10.2210/pdb9Y9Y/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-15 Released: 2025-09-24
Deposition Author(s): 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: 3.03 Å
R-Value Free:
0.268 (Depositor), 0.266 (DCC)
R-Value Work:
0.230 (Depositor), 0.230 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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Literature

Crystal structure of DNA integrity scanning protein DisA from Mycobacterium tuberculosis in complex with cyclic di-AMP and bromide

Liu, L., Lovell, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 318.79 kDa
Atom Count: 20,018
Modeled Residue Count: 2,626
Deposited Residue Count: 2,880
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA integrity scanning protein DisA	A, B, C, D, E A, B, C, D, E, F, G, H	360	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: disA, dacA, Rv3586 EC: 2.7.7.85
UniProt
Find proteins for P9WNW5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNW5 Go to UniProtKB: P9WNW5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WNW5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2BA (Subject of Investigation/LOI) Query on 2BA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth E] SDF format, chain T [auth G] SDF format, chain V [auth H] MOL2 format, chain I [auth A] MOL2 format, chain P [auth E] MOL2 format, chain T [auth G] MOL2 format, chain V [auth H] mmCIF format, chain I [auth A] mmCIF format, chain P [auth E] mmCIF format, chain T [auth G] mmCIF format, chain V [auth H]	I [auth A], P [auth E], T [auth G], V [auth H]	(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide C₂₀ H₂₄ N₁₀ O₁₂ P₂ PDXMFTWFFKBFIN-XPWFQUROSA-N		Interactions Focus chain I [auth A] Focus chain P [auth E] Focus chain T [auth G] Focus chain V [auth H] Interactions & Density Focus chain I [auth A] Focus chain P [auth E] Focus chain T [auth G] Focus chain V [auth H]
BR (Subject of Investigation/LOI) Query on BR Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain W [auth H] SDF format, chain U [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain W [auth H] MOL2 format, chain U [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain W [auth H] mmCIF format, chain U [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B]	J [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] J [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain R [auth E] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth E] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth E]	L [auth B], N [auth C], R [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Focus chain N [auth C] Focus chain R [auth E] Interactions & Density Focus chain L [auth B] Focus chain N [auth C] Focus chain R [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free: 0.268 (Depositor), 0.266 (DCC)
R-Value Work: 0.230 (Depositor), 0.230 (DCC)
R-Value Observed: 0.232 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 279.207	α = 90
b = 74.64	β = 125.89
c = 197.795	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

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