9Y4S | pdb_00009y4s

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

PDB DOI: https://doi.org/10.2210/pdb9Y4S/pdb

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

Deposited: 2025-09-03 Released: 2025-09-17
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: 2.89 Å
R-Value Free:
0.252 (Depositor), 0.249 (DCC)
R-Value Work:
0.203 (Depositor), 0.208 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: in silico
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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

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

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

To be published.

Macromolecule Content

Total Structure Weight: 318.89 kDa
Atom Count: 20,342
Modeled Residue Count: 2,678
Deposited Residue Count: 2,880
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WNW5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 BA [auth H] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain Y [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain Y [auth G]	BA [auth H], T [auth E], V [auth F], Y [auth G]	(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 BA [auth H] Focus chain T [auth E] Focus chain V [auth F] Focus chain Y [auth G] Interactions & Density Focus chain BA [auth H] Focus chain T [auth E] Focus chain V [auth F] Focus chain Y [auth G]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain W [auth G] SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain AA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain W [auth G] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain AA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain W [auth G] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	AA [auth H] I [auth A] J [auth A] K [auth A] M [auth B] AA [auth H], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth C], Q [auth D], R [auth D], S [auth E], U [auth F], W [auth G], X [auth G], Z [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain X [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.252 (Depositor), 0.249 (DCC)
R-Value Work: 0.203 (Depositor), 0.208 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 277.526	α = 90
b = 74.263	β = 126.05
c = 199.413	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

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-17

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