PDB-9y4s: Crystal structure of DNA integrity scanning protein (DisA) from M...

ID or keywords:

Entry

Database: PDB / ID: 9y4s

Title

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

Components

DNA integrity scanning protein DisA

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / DisA

Function / homology

Function and homology information

diadenylate cyclase / diadenylate cyclase activity / adenylate cyclase activity / DNA repair / DNA binding / ATP binding
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.89 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of DNA integrity scanning protein (DisA) from Mycobacterium tuberculosis in complex with cyclic di-AMP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Sep 3, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9y4s.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb9y4s.ent.gz	852.6 KB	Display	PDB format
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Others	Other downloads

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Validation report

Summary document	9y4s_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	9y4s_full_validation.pdf.gz	2 MB	Display
Data in XML	9y4s_validation.xml.gz	100.3 KB	Display
Data in CIF	9y4s_validation.cif.gz	128 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y4/9y4s ftp://data.pdbj.org/pub/pdb/validation_reports/y4/9y4s	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#55 - Jul 2004 DNA Ligase similarity (1)

Deposited unit

A: DNA integrity scanning protein DisA

B: DNA integrity scanning protein DisA

C: DNA integrity scanning protein DisA

D: DNA integrity scanning protein DisA

E: DNA integrity scanning protein DisA

F: DNA integrity scanning protein DisA

G: DNA integrity scanning protein DisA

H: DNA integrity scanning protein DisA

hetero molecules

319 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	277.526, 74.263, 199.413
Angle α, β, γ (deg.)	90.00, 126.05, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	DNA integrity scanning protein DisA / Cyclic-di-AMP synthase / c-di-AMP synthase / Diadenylate cyclase Mass: 39426.461 Da / Num. of mol.: 8 / Fragment: T5-S356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: disA, dacA, Rv3586 / Plasmid: MytuD.17706.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNW5, diadenylate cyclase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Chemical	ChemComp-2BA / (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 / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate Mass: 658.412 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.3 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpheus Fusion F12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose ...Details: Morpheus Fusion F12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose and 20 mM N-Acetyl-D-Glucosamine. MytuD.17706.a.B2.PW39404 at 13.1 mg/mL. Screened as apo protein but cyclic di-AMP was bound to 4 sites likely acquired from the expression host. plate 19976 F12 drop 2, Puck: PSL-2416, Cryo: direct

Crystal

Density Matthews: 2.63 Å³/Da / Density % sol: 53.3 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus Fusion F12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 3, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.89→49.22 Å / Num. obs: 74055 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC_1/2: 0.997 / R_merge(I) obs: 0.164 / R_pim(I) all: 0.068 / R_rim(I) all: 0.178 / Χ²: 1.15 / Net I/σ(I): 11.5 / Num. measured all: 507379
Reflection shell	Resolution: 2.89→2.97 Å / % possible obs: 100 % / Redundancy: 7.2 % / R_merge(I) obs: 1.543 / Num. measured all: 39545 / Num. unique obs: 5463 / CC_1/2: 0.502 / R_pim(I) all: 0.614 / R_rim(I) all: 1.663 / Χ²: 1.01 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5794: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.89→49.22 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2522	3725	5.03 %
R_work	0.2028	-	-
obs	0.2053	74044	99.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.89→49.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20129	0	213	0	20342

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	20582
X-RAY DIFFRACTION	f_angle_d	0.757	27973
X-RAY DIFFRACTION	f_dihedral_angle_d	11.208	7753
X-RAY DIFFRACTION	f_chiral_restr	0.043	3362
X-RAY DIFFRACTION	f_plane_restr	0.007	3653

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.89-2.93	0.3248	131	0.2795	2612	X-RAY DIFFRACTION	100
2.93-2.97	0.3029	153	0.2769	2568	X-RAY DIFFRACTION	100
2.97-3.01	0.33	155	0.273	2544	X-RAY DIFFRACTION	100
3.01-3.05	0.366	134	0.2815	2609	X-RAY DIFFRACTION	100
3.05-3.09	0.3152	130	0.2759	2605	X-RAY DIFFRACTION	100
3.09-3.14	0.3112	137	0.2851	2548	X-RAY DIFFRACTION	100
3.14-3.19	0.3611	139	0.2789	2614	X-RAY DIFFRACTION	100
3.19-3.25	0.3348	123	0.2661	2588	X-RAY DIFFRACTION	100
3.25-3.31	0.3166	139	0.2494	2578	X-RAY DIFFRACTION	100
3.31-3.37	0.274	122	0.2219	2625	X-RAY DIFFRACTION	100
3.37-3.44	0.2604	153	0.2146	2537	X-RAY DIFFRACTION	100
3.44-3.52	0.2632	111	0.1998	2657	X-RAY DIFFRACTION	100
3.52-3.6	0.2576	148	0.1999	2550	X-RAY DIFFRACTION	100
3.6-3.69	0.27	150	0.2104	2613	X-RAY DIFFRACTION	100
3.69-3.79	0.2712	147	0.2113	2582	X-RAY DIFFRACTION	100
3.79-3.9	0.2742	132	0.2071	2590	X-RAY DIFFRACTION	100
3.9-4.02	0.2458	132	0.1814	2601	X-RAY DIFFRACTION	100
4.02-4.17	0.1893	138	0.1749	2598	X-RAY DIFFRACTION	100
4.17-4.33	0.2404	114	0.1657	2645	X-RAY DIFFRACTION	100
4.33-4.53	0.2101	138	0.1602	2581	X-RAY DIFFRACTION	100
4.53-4.77	0.2008	149	0.1546	2597	X-RAY DIFFRACTION	100
4.77-5.07	0.2229	143	0.1685	2616	X-RAY DIFFRACTION	100
5.07-5.46	0.2414	115	0.1945	2614	X-RAY DIFFRACTION	100
5.46-6.01	0.2856	151	0.2287	2632	X-RAY DIFFRACTION	100
6.01-6.87	0.2629	152	0.2212	2642	X-RAY DIFFRACTION	100
6.88-8.65	0.2242	134	0.1945	2649	X-RAY DIFFRACTION	100
8.66-49.22	0.2213	155	0.1854	2724	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	6.1219	0.0085	0.5459	3.1421	0.9379	4.2669	-0.3155	-0.5775	-0.3329	0.2785	0.2814	0.1827	0.2303	-0.0298	0.0204	0.4411	0.0897	0.0578	0.3095	0.0252	0.4408	18.7422	-31.0967	-29.0433
2	1.0984	-0.2991	-0.2038	2.5531	-1.65	3.1757	0.0201	0.0886	-0.0215	0.2762	0.2889	0.4329	-0.2907	-0.4108	-0.2865	0.4949	0.0143	0.1395	0.6321	0.096	0.685	24.073	-28.396	16.7544
3	3.3847	-0.0831	-0.7483	4.5572	-0.2952	3.4555	0.2247	-0.1463	-0.0238	0.6678	-0.2561	0.2745	-0.0371	-0.0348	-0.0002	0.4361	-0.0388	0.0419	0.314	-0.0621	0.3234	9.8919	2.8642	-25.0118
4	1.0073	0.5061	-0.5804	1.5797	0.2891	3.3781	0.0921	-0.07	-0.0699	0.093	-0.1264	-0.0406	0.0891	-0.0005	0.0319	0.4319	0.0103	-0.0063	0.4495	0.0877	0.4919	24.8367	3.1293	19.8404
5	5.5248	0.1716	-0.3725	2.73	-0.5194	4.9301	0.0076	-0.2728	0.2298	0.1291	0.1435	-0.2882	-0.2057	0.2814	-0.1339	0.329	0.0413	-0.0158	0.2705	-0.028	0.411	43.7032	11.6774	-29.7504
6	6.6331	-0.0857	2.397	1.6477	-0.1585	4.1457	-0.146	-0.7178	0.0774	0.3243	0.0417	-0.1797	0.0799	-0.1251	0.1084	0.4396	0.0208	-0.0491	0.5337	-0.0125	0.4923	57.7979	1.4699	5.3234
7	1.16	-0.7793	0.0413	4.9461	-0.4031	1.117	0.3532	0.1372	0.0471	1.3871	-0.1807	0.3707	0.0973	-0.5825	-0.1948	1.157	0.1166	-0.0815	1.2024	-0.1271	0.9324	61.5025	14.1841	26.7664
8	2.643	1.2036	0.0018	4.0512	0.672	2.8093	0.2559	-0.0994	-0.6469	0.248	-0.143	-0.6016	0.07	0.0758	-0.1072	0.3516	0.0497	-0.0756	0.3704	0.1042	0.5806	52.4254	-22.2538	-34.142
9	2.1607	-0.1971	0.1942	1.5724	-0.3701	4.4563	0.0708	-0.1798	-0.1551	0.1401	-0.148	-0.0804	-0.153	0.331	0.0872	0.3635	-0.0129	-0.0115	0.4478	0.0688	0.4008	51.6314	-34.5442	7.2659
10	4.2157	-0.8445	-2.2221	5.4437	1.0659	4.9836	0.046	-1.0384	0.2823	0.1399	0.2498	-0.3969	-0.1207	0.9395	-0.3041	0.5505	-0.0287	-0.05	1.122	0.0893	0.6429	67.4319	-32.7523	27.0035
11	5.0509	-1.023	-0.9392	1.7323	0.2223	3.1246	0.0072	0.3468	0.0103	-0.1827	0.0415	0.0527	-0.038	-0.2305	-0.0373	0.4408	0.0216	-0.0354	0.3193	-0.0016	0.3432	19.6735	15.0132	-48.9127
12	2.0358	0.2841	1.5802	2.5244	-1.3764	5.6345	0.1679	0.7877	-0.2453	-0.675	0.2454	0.3937	0.2695	-0.4564	-0.4007	0.963	0.1874	-0.08	1.0946	0.0311	0.7025	11.2162	2.6856	-83.9548
13	1.6563	-1.326	0.0989	4.7142	-5.0246	6.5432	-0.0625	0.106	-0.2051	-0.0172	0.6461	0.6064	-0.0728	-1.103	-0.539	1.0695	0.1361	-0.1611	1.5959	0.5055	1.1314	-2.8781	11.8905	-93.903
14	3.0458	0.2261	-1.2004	3.5358	-0.8477	4.9039	0.0534	0.2837	-0.198	-0.2074	-0.1078	0.2748	-0.08	-0.4137	0.0595	0.3493	0.0278	-0.0587	0.4045	-0.1406	0.4712	4.0063	-16.4673	-48.6392
15	0.6798	0.1421	0.865	2.3183	1.0946	5.8131	-0.1265	1.3446	-0.2068	-0.4586	0.1575	-0.1834	-0.4845	0.1305	0.0282	0.6452	-0.0579	-0.0885	1.2574	-0.1908	0.6888	8.7154	-18.0074	-82.9576
16	2.4525	1.2659	1.1811	2.3323	0.2113	2.7374	-0.0007	-0.0974	-0.0687	-0.8244	0.423	-0.0557	0.4786	-1.1902	-0.6036	1.2208	-0.2562	-0.1056	1.6371	-0.2879	0.7623	-4.64	-28.1052	-91.2521
17	3.6775	-2.0724	2.6424	9.4488	4.0435	5.647	0.5378	0.5273	-0.5068	1.188	-0.7435	1.0225	0.5616	1.1996	0.3703	1.4031	-0.0284	-0.1024	1.4024	0.0102	0.9071	-13.914	-23.2735	-107.6888
18	4.1611	2.6875	-0.8287	2.0194	0.1321	6.9268	-0.0794	0.7853	-0.0643	0.1104	-0.1563	0.3082	0.7251	-0.1085	0.2666	0.5537	0.0632	0.0225	0.4133	0.1283	0.6217	28.7595	-27.3115	-61.7055
19	4.4146	0.2419	0.0659	2.3207	0.1586	3.5064	0.1052	0.1691	-0.1504	0.0271	-0.0334	-0.1092	0.2069	0.0401	-0.0664	0.445	0.0612	0.0791	0.3101	-0.0056	0.465	34.3329	-34.8737	-50.6016
20	6.6384	-0.8547	1.4877	3.5287	-0.0289	4.8527	-0.0643	0.9401	0.1398	-0.2625	-0.0789	-0.2977	-0.079	0.3589	0.069	0.4799	0.0265	0.1433	0.4159	0.0487	0.589	40.6268	-27.2302	-57.8975
21	1.1157	0.6013	-2.8795	0.4708	-1.4919	7.5223	-0.5011	1.0735	0.354	-0.3781	-0.0166	0.1034	-1.348	-1.0078	0.1769	1.2056	-0.1496	-0.0504	1.3275	0.2134	0.7874	29.6879	-15.2791	-91.4101
22	1.3046	-0.9311	0.2997	1.4451	1.5228	5.3453	-0.4322	1.1324	-0.1049	-0.9056	0.1637	-0.103	-0.3773	0.7418	0.2285	1.0968	-0.2253	0.0636	1.2883	0.1071	0.7346	33.1496	-25.3452	-91.1604
23	4.1886	-3.941	4.901	3.961	-4.8961	6.2118	-0.0718	1.9927	1.1745	-0.7481	-1.6722	-1.958	0.4406	0.3275	1.5935	0.9721	-0.1794	0.2069	1.421	0.0659	1.0918	46.6896	-20.8365	-95.6113
24	1.207	-0.6848	1.5576	3.3433	-1.1755	4.0119	-0.3636	0.1159	-0.2904	-0.9204	0.2323	-0.1733	0.7718	0.7396	0.1765	1.6351	-0.2928	0.0487	1.6462	0.0336	0.85	32.5996	-30.0659	-110.6442
25	0.9626	1.4154	-0.668	2.1332	-1.0869	0.6759	-0.8025	1.1619	-0.4339	-0.3442	1.4661	-0.8446	0.7178	-1.0855	-0.6561	0.7179	-0.3125	-0.286	1.8681	-0.3531	0.5849	20.767	-34.3341	-118.8887
26	3.5994	0.9033	-0.1105	3.9528	1.4521	4.6517	0.2566	0.3035	0.0427	-0.5633	0.1036	-0.3449	-0.3479	0.1953	-0.2905	0.5028	0.0627	0.1501	0.4572	0.0853	0.4675	51.1965	0.2359	-54.9425
27	1.1082	0.3724	-2.0158	0.4853	0.534	6.0146	0.2834	0.6637	0.3375	-0.1536	0.1641	0.0941	-0.6141	-1.1433	-0.4427	1.1568	0.2813	0.0196	1.2804	0.1491	0.8538	33.971	6.007	-99.0678

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 143 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 144 through 353 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 6 through 143 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 144 through 354 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 6 through 143 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 144 through 286 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 287 through 354 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 7 through 143 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 144 through 323 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 324 through 354 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 6 through 143 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 144 through 225 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 226 through 332 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 7 through 143 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 144 through 224 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 225 through 315 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 316 through 351 )
18	X-RAY DIFFRACTION	18	chain 'G' and (resid 7 through 32 )
19	X-RAY DIFFRACTION	19	chain 'G' and (resid 33 through 102 )
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 103 through 143 )
21	X-RAY DIFFRACTION	21	chain 'G' and (resid 144 through 182 )
22	X-RAY DIFFRACTION	22	chain 'G' and (resid 183 through 260 )
23	X-RAY DIFFRACTION	23	chain 'G' and (resid 261 through 274 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 275 through 323 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 324 through 347 )
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 7 through 143 )
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 144 through 348 )

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