PDB-6lhx: Crystal structure of ThsA

ID or keywords:

Entry

Database: PDB / ID: 6lhx

Title

Crystal structure of ThsA

Components

ThsA

Keywords

HYDROLASE / NAD+ hydrolysis

Function / homology

Function and homology information

NAD+ glycohydrolase / defense response to virus /

hydrolase activity /

nucleotide binding /

cytoplasm
Similarity search - Function

Biological species

Bacillus cereus MSX-D12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.501 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6lhx.cif.gz	683 KB	Display	PDBx/mmCIF format
PDB format	pdb6lhx.ent.gz	581.8 KB	Display	PDB format
PDBx/mmJSON format	6lhx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lh/6lhx ftp://data.pdbj.org/pub/pdb/validation_reports/lh/6lhx	HTTPS FTP

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Related structure data

Related structure data	6lhyC C: citing same article (ref.)
Similar structure data	6tur-d 3bg7-2 5ume-d 429 4163 2rgr-1 7k2x-d 2igk-2 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
Related items in Molecule of the Month	#213 - Sep 2017 Sirtuins similarity (3) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: ThsA

B: ThsA

C: ThsA

D: ThsA

222 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, light scattering

Unit cell

Length a, b, c (Å)	180.424, 168.584, 93.614
Angle α, β, γ (deg.)	90.000, 106.710, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain A	A	2 - 476
2	1	1	chain B	B	2 - 476
3	1	1	chain C	C	2 - 475
4	1	1	chain D	D	2 - 475

#1: Protein	ThsA Mass: 55569.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Bacillus cereus MSX-D12 (bacteria) / Gene: II9_05448 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J8G6Z1
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 3.37 Å³/Da / Density % sol: 63.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22% PPG400, 0.1 M MES pH 6.5, 0.2 M MgCl2

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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: 2.5→50 Å / Num. obs: 181015 / % possible obs: 99.6 % / Redundancy: 7.3 % / B_iso Wilson estimate: 63.54 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.14 / R_pim(I) all: 0.055 / Net I/σ(I): 10.54
Reflection shell	Resolution: 2.5→2.59 Å / R_merge(I) obs: 1.666 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 9063 / CC_1/2: 0.543 / R_pim(I) all: 0.665 / % possible all: 99.1

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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
BUCCANEER		model building
HKL-2000		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 2.501→31.641 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2727	3958	2.19 %
R_work	0.2417	177057	-
obs	0.2424	181015	99.21 %

Solvent computation

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

Displacement parameters

B_iso max: 329.3 Å² / B_iso mean: 82.1693 Å² / B_iso min: 32.32 Å²

Refinement step

Cycle: final / Resolution: 2.501→31.641 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13296	0	0	36	13332
B_iso mean	-	-	-	55.14	-
Num. residues	-	-	-	-	1726

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	13534
X-RAY DIFFRACTION	f_angle_d	0.81	18340
X-RAY DIFFRACTION	f_chiral_restr	0.032	2093
X-RAY DIFFRACTION	f_plane_restr	0.004	2364
X-RAY DIFFRACTION	f_dihedral_angle_d	13.163	4762

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	7397	X-RAY DIFFRACTION	9.89	TORSIONAL
1	2	B	7397	X-RAY DIFFRACTION	9.89	TORSIONAL
1	3	C	7397	X-RAY DIFFRACTION	9.89	TORSIONAL
1	4	D	7397	X-RAY DIFFRACTION	9.89	TORSIONAL

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 (%)
2.5012-2.5317	0.349	137	0.341	6049	94
2.5317-2.5638	0.3954	137	0.3369	6211	98
2.5638-2.5975	0.3835	142	0.3313	6270	98
2.5975-2.633	0.374	140	0.3347	6270	99
2.633-2.6706	0.3955	140	0.3337	6262	99
2.6706-2.7105	0.3559	139	0.3344	6305	99
2.7105-2.7528	0.3804	143	0.3227	6384	99
2.7528-2.7979	0.3719	138	0.3212	6263	99
2.7979-2.8461	0.3643	139	0.3158	6283	99
2.8461-2.8979	0.3179	140	0.2986	6285	99
2.8979-2.9536	0.3247	146	0.297	6378	99
2.9536-3.0138	0.3417	142	0.2971	6369	99
3.0138-3.0793	0.3665	138	0.293	6261	99
3.0793-3.1508	0.3202	146	0.2798	6382	99
3.1508-3.2296	0.3041	140	0.2806	6352	100
3.2296-3.3168	0.3286	140	0.2723	6343	100
3.3168-3.4143	0.3033	140	0.2489	6322	100
3.4143-3.5244	0.2802	143	0.2462	6385	100
3.5244-3.6501	0.2935	145	0.2323	6346	100
3.6501-3.7961	0.2416	140	0.2326	6337	100
3.7961-3.9685	0.2136	144	0.2233	6426	100
3.9685-4.1773	0.2738	141	0.2116	6344	100
4.1773-4.4384	0.2489	143	0.2068	6402	100
4.4384-4.78	0.1911	142	0.1918	6359	100
4.78-5.259	0.2336	144	0.2023	6358	100
5.259-6.0155	0.2754	143	0.2334	6398	100
6.0155-7.5618	0.3128	143	0.2463	6359	100
7.5618-31.641	0.1923	143	0.2067	6354	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	1.4312	1.1242	1.5481	3.9572	1.2267	1.9229	-0.1674	0.4112	0.1353	-0.3272	0.0251	-0.0068	-0.0533	-0.1082	0.1881	0.4651	0.0138	0.1308	0.5711	0.0444	0.3902	-24.7185	23.4043	-9.747
2	2.9506	0.0357	-1.1978	1.4198	0.4102	3.2418	-0.3469	0.5389	-0.2785	-0.0189	0.0154	0.14	0.6905	-0.5114	0.2985	0.6453	-0.1405	0.1082	0.4967	-0.061	0.417	-33.7342	9.176	-6.5766
3	3.9019	0.2635	1.5147	5.8191	1.5842	6.7264	-0.3119	0.9457	-0.1022	-0.7686	-0.1021	0.3521	0.3807	-0.598	0.4148	0.6385	-0.1563	0.1797	0.8792	-0.0781	0.5212	-58.5357	12.0181	5.6255
4	4.2031	1.9759	2.026	6.7374	1.0067	3.6115	0.092	-0.5647	-0.7521	0.3516	-0.0894	-0.2408	0.8041	-0.1563	-0.033	0.6041	-0.0413	0.2095	0.5916	0.1494	0.5255	-17.3965	3.1948	17.638
5	5.5509	0.0081	1.1832	0.7117	0.005	0.0825	-0.0588	-0.4684	-0.0737	0.0485	0.0553	-0.082	-0.0447	0.1068	0.0503	0.5531	0.0107	0.1511	0.6308	0.0817	0.409	-6.579	12.304	20.4203
6	3.0281	-2.4509	-0.1295	1.969	0.1172	0.0774	0.0327	-1.0755	1.4176	1.0313	0.1191	0.4662	-0.5616	-0.3836	0.0701	0.7251	0.0089	0.1658	0.9481	-0.3721	0.9093	-49.2497	31.2022	31.9122
7	4.2868	0.3428	0.4196	3.0764	0.0653	4.3382	0.0397	-1.1105	0.2837	0.3701	-0.1336	-0.0706	0.3886	0.2763	0.1425	0.6477	-0.04	0.225	1.069	-0.1422	0.4953	-42.4409	20.2286	33.1403
8	2.1831	-0.5155	0.5599	2.8813	-0.6454	2.2099	-0.0954	-0.5049	0.1602	0.3473	0.1045	0.1564	-0.0832	-0.2135	-0.0403	0.4667	0.0362	0.1622	0.4883	-0.0232	0.4383	-22.3278	46.6075	9.1666
9	2.4047	-0.0584	0.8186	1.0295	0.5972	2.6881	-0.3305	-1.0581	0.1802	0.14	0.0896	0.2108	-0.5193	-0.9575	0.145	0.6931	0.2295	0.2067	0.7381	-0.1514	0.7607	-40.3645	60.0218	9.1455
10	6.2341	0.0978	-0.5445	3.4359	0.4128	6.5183	-0.1012	-0.4951	-0.7396	0.3452	-0.2548	0.6221	-0.1856	-0.9847	0.3819	0.6226	0.1656	0.1016	0.7452	-0.1341	0.8401	-57.5835	56.4872	-9.0575
11	5.5722	-0.8343	-0.8688	2.2906	0.3334	3.5623	0.0245	0.8038	1.1049	-0.5087	-0.0579	0.0912	-0.8349	0.0687	0.0797	0.5619	0.0131	0.0153	0.416	0.2328	0.6074	-15.5215	63.2245	-17.0253
12	6.1134	-0.4429	-0.5499	1.0888	0.6614	1.7341	-0.0474	1.0973	0.3007	-0.3669	-0.1278	-0.1235	-0.347	0.4733	0.0575	0.6592	0.0359	0.0871	0.66	0.1535	0.5238	-5.8696	54.0664	-23.4411
13	5.175	-0.1779	-2.5782	4.1544	1.0924	5.9963	-0.0448	1.5558	-0.9971	-0.6067	-0.3709	0.1961	-0.0035	-0.7017	0.3771	0.6913	0.1639	0.0327	1.0305	-0.3527	0.8231	-42.4863	48.1688	-35.1842

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 2 through 164 )	A	2 - 164
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 165 through 340 )	A	165 - 340
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 341 through 476 )	A	341 - 476
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 176 )	B	2 - 176
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 177 through 288 )	B	177 - 288
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 289 through 315 )	B	289 - 315
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 316 through 476 )	B	316 - 476
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 2 through 220 )	C	2 - 220
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 221 through 315 )	C	221 - 315
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 316 through 475 )	C	316 - 475
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 2 through 202 )	D	2 - 202
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 203 through 290 )	D	203 - 290
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 291 through 475 )	D	291 - 475

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