PDB-6lhy: Crystal structure of ThsB

ID or keywords:

Entry

Database: PDB / ID: 6lhy

Title

Crystal structure of ThsB

Components

DUF1863 domain-containing protein

Keywords

UNKNOWN FUNCTION / TIR-like domain

Function / homology

Thoeris protein ThsB, TIR-like domain superfamily / Thoeris protein ThsB, TIR-like domain / Thoeris protein ThsB, TIR-like domain / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response to virus / hydrolase activity / cytoplasm / Putative cyclic ADP-D-ribose synthase ThsB1

Function and homology information

Biological species

Bacillus cereus MSX-D12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.796 Å

Authors

Bae, E. / Ka, D. / Oh, H.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Nat Commun / Year: 2020
Title: Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD+degradation.
Authors: Ka, D. / Oh, H. / Park, E. / Kim, J.H. / Bae, E.

History

Deposition	Dec 10, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 24, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6lhy.cif.gz	164.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6lhy.ent.gz	129.9 KB	Display	PDB format
PDBx/mmJSON format	6lhy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6lhy_validation.pdf.gz	430 KB	Display	wwPDB validaton report
Full document	6lhy_full_validation.pdf.gz	431.4 KB	Display
Data in XML	6lhy_validation.xml.gz	17.6 KB	Display
Data in CIF	6lhy_validation.cif.gz	26 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lh/6lhy ftp://data.pdbj.org/pub/pdb/validation_reports/lh/6lhy	HTTPS FTP

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Related structure data

Related structure data	6lhxC C: citing same article (ref.)
Similar structure data	6hfo-d 4od7-2 6ndv-d 2xh3-2 5kl2-d 3hnm-3 4csr-d 1htj-d 1r4v-d 3a4s-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: DUF1863 domain-containing protein

B: DUF1863 domain-containing protein

45.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DUF1863 domain-containing protein

defined by author
Evidence: light scattering
22.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DUF1863 domain-containing protein

defined by author
22.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.570, 67.731, 59.169
Angle α, β, γ (deg.)	90.000, 92.380, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DUF1863 domain-containing protein / ThsB Mass: 22641.252 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus MSX-D12 (bacteria) / Gene: II9_05449 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J8G8J6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.07 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3 M NaCl, 0.1 M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9791 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 12, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.796→50 Å / Num. obs: 39424 / % possible obs: 99 % / Redundancy: 3.8 % / B_iso Wilson estimate: 21.25 Å² / CC_1/2: 0.941 / R_merge(I) obs: 0.092 / R_pim(I) all: 0.055 / Net I/σ(I): 12.35
Reflection shell	Resolution: 1.8→1.86 Å / R_merge(I) obs: 0.605 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 7689 / CC_1/2: 0.761 / R_pim(I) all: 0.361

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data collection
HKL-2000		data scaling
AutoSol		phasing
PDB_EXTRACT	3.25	data extraction
PHENIX		model building
HKL-2000		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 1.796→29.559 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.66 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2258	1986	5.1 %
R_work	0.1907	36920	-
obs	0.1925	38906	98.41 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 78.02 Å² / B_iso mean: 28.6425 Å² / B_iso min: 11.51 Å²

Refinement step

Cycle: final / Resolution: 1.796→29.559 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2836	0	0	332	3168
B_iso mean	-	-	-	33.07	-
Num. residues	-	-	-	-	350

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2930
X-RAY DIFFRACTION	f_angle_d	0.951	3972
X-RAY DIFFRACTION	f_chiral_restr	0.043	407
X-RAY DIFFRACTION	f_plane_restr	0.004	503
X-RAY DIFFRACTION	f_dihedral_angle_d	11.92	1023

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.796-1.8405	0.2832	122	0.2469	2429	91
1.8405-1.8903	0.2613	156	0.2262	2551	97
1.8903-1.9459	0.2626	130	0.2089	2574	97
1.9459-2.0087	0.2049	136	0.1948	2614	98
2.0087-2.0805	0.2179	148	0.1942	2650	99
2.0805-2.1637	0.2374	153	0.1909	2635	99
2.1637-2.2622	0.2624	135	0.1955	2653	99
2.2622-2.3814	0.238	139	0.2011	2646	99
2.3814-2.5305	0.2333	147	0.2122	2671	99
2.5305-2.7258	0.2545	138	0.2057	2668	100
2.7258-2.9999	0.2619	149	0.2161	2684	100
2.9999-3.4334	0.202	142	0.1892	2683	100
3.4334-4.3235	0.2129	145	0.1534	2703	100
4.3235-29.559	0.1939	146	0.1791	2759	100

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	2.0699	-6.6638	3.0592	4.2381	-2.3844	6.0506	0.1995	0.4207	0.4424	-0.3064	-0.1814	-0.356	0.0299	0.1132	-0.0271	0.2507	-0.0738	0.0549	0.1433	0.0096	0.2395	24.668	28.3902	33.179
2	7.8862	-0.1352	2.5468	4.2558	-0.4214	3.7507	-0.1997	0.4848	0.0928	-0.2674	0.2421	-0.3963	-0.4881	0.373	0.0226	0.2651	-0.0518	0.0371	0.1956	-0.0115	0.2515	29.9186	34.2038	37.0415
3	2.8203	0.1088	1.839	4.4519	1.2364	5.4833	-0.1797	0.8957	-0.0703	-0.7092	0.2994	-0.7678	-0.212	0.5037	-0.1189	0.4012	-0.0842	0.1323	0.3613	-0.0411	0.3409	33.995	30.7638	33.0548
4	2.0149	0.8888	-4.3023	5.8338	-0.6947	4.6173	-0.6046	1.0124	0.0909	-1.8489	0.8655	-0.6079	0.0615	0.1548	-0.1895	0.6789	-0.1356	0.224	0.3399	-0.0588	0.3912	32.2431	16.6988	25.9025
5	2.8894	-1.5473	-0.2153	4.2287	0.5278	1.8959	0.0145	0.0994	0.004	-0.2407	0.0241	-0.2628	0.0165	0.0815	-0.0292	0.155	-0.0314	0.0335	0.122	-0.0025	0.1098	22.8437	20.6856	38.2248
6	5.7407	-3.2489	1.6831	3.163	-0.6469	4.9615	0.4197	0.3318	-0.7677	-0.2528	-0.329	0.3299	0.8118	0.0323	-0.0358	0.3094	-0.0189	0.039	0.1295	-0.0405	0.2715	21.6378	2.3625	38.4569
7	4.3051	-3.0221	1.666	3.9998	-1.6408	7.392	0.2159	0.3922	-0.1857	-0.1608	-0.2972	-0.1218	0.5156	0.9795	0.0955	0.2608	0.0174	0.063	0.2356	0.0031	0.2399	31.1843	3.6167	37.8554
8	2.978	-2.3573	-0.4803	8.2759	-0.5953	2.1454	-0.1978	-0.2554	-0.2047	0.5461	0.0936	0.0323	0.2202	0.163	0.0772	0.1736	0.0112	0.0094	0.1803	0.0104	0.0942	25.3601	15.218	48.3367
9	4.7326	3.1342	-3.8634	9.8621	1.9172	2.0534	0.0035	-0.1233	0.0529	0.4458	0.1832	-0.8204	-0.4601	1.0413	-0.2282	0.3079	-0.0209	-0.0722	0.3225	0.0165	0.3242	32.4836	31.3981	47.7198
10	1.882	0.2895	1.0247	4.889	0.4791	7.712	-0.0931	0.1829	-0.2221	-0.0792	0.2627	-0.1766	-0.0202	0.1406	-0.2411	0.0909	-0.0071	0.0511	0.1323	-0.0324	0.1985	48.0251	-21.6936	60.3036
11	1.7519	0.89	2.4477	6.6711	3.9131	4.6708	0.3052	0.8513	-0.2163	-0.5964	0.4042	-0.3142	-0.0143	0.3478	-0.5777	0.2236	-0.0045	0.0613	0.3196	-0.0536	0.3307	44.9919	-26.4519	53.9646
12	7.4101	0.8185	-3.1356	4.005	-1.9041	7.0741	-0.8014	1.225	-0.1793	-0.8608	0.7919	-0.8574	0.8129	1.2879	-0.0223	0.5455	-0.1277	0.2879	0.6815	-0.1259	0.5074	53.7307	-9.5583	51.3476
13	2.7643	-0.2699	0.2205	3.6088	-0.3924	2.3528	-0.0754	0.298	0.0833	-0.3546	0.1263	-0.1632	-0.0772	0.1203	-0.0349	0.1442	-0.0243	0.0326	0.1471	-0.011	0.1538	42.6394	-13.8516	62.0915
14	5.278	-2.9377	3.9101	8.5884	-8.9745	2.2084	-0.2295	0.031	0.5748	0.8016	-0.2122	-0.2819	-1.3005	0.2123	0.536	0.3518	-0.005	0.0102	0.1627	-0.0059	0.2686	41.1624	5.2182	62.5006
15	5.8538	-5.7996	2.2249	5.8675	-2.6109	1.7253	0.3229	0.7466	0.3581	-0.1317	-0.6587	-0.3754	-0.0012	0.337	0.42	0.2157	-0.0256	0.062	0.2322	0.0428	0.2546	42.1034	5.316	52.3466
16	1.153	-3.6023	1.602	2.0257	-4.9301	2.4128	-0.1561	-0.0273	-0.1003	0.2622	0.3077	0.53	-0.4418	-0.4211	-0.2239	0.3151	0.0642	0.0382	0.2343	0.0437	0.2606	31.3539	2.6679	59.5141
17	0.8878	-1.1788	-0.039	2.0399	-3.8507	2.662	-0.0273	0.2783	-0.1571	-0.0251	0.1758	0.7929	0.147	-0.3089	-0.2162	0.1743	-0.0233	-0.0025	0.2046	0.0182	0.2625	32.8759	-20.6091	61.2337
18	2.0464	6.6586	-8.468	2.0616	-6.6903	2.0331	-0.3919	0.9895	-0.5107	-1.0923	0.5169	-0.1622	0.5752	-0.8015	-0.105	0.3844	-0.046	-0.0589	0.3829	-0.0635	0.3124	33.7206	-26.2219	54.4793

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 18 )	A	3 - 18
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 27 )	A	19 - 27
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 28 through 52 )	A	28 - 52
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 53 through 62 )	A	53 - 62
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 63 through 126 )	A	63 - 126
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 127 through 145 )	A	127 - 145
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 146 through 159 )	A	146 - 159
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 160 through 182 )	A	160 - 182
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 183 through 192 )	A	183 - 192
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 18 )	B	2 - 18
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 19 through 52 )	B	19 - 52
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 53 through 62 )	B	53 - 62
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 63 through 126 )	B	63 - 126
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 127 through 145 )	B	127 - 145
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 146 through 159 )	B	146 - 159
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 160 through 171 )	B	160 - 171
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 172 through 182 )	B	172 - 182
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 183 through 192 )	B	183 - 192

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