PDB-8hyn: Bacterial STING from Riemerella anatipestifer

ID or keywords:

Entry

Database: PDB / ID: 8hyn

Title

Bacterial STING from Riemerella anatipestifer

Components

CD-NTase-associated protein 12

Keywords

SIGNALING PROTEIN / CD-NTase-associated protein 12

Function / homology

:

Function and homology information

Biological species

Riemerella anatipestifer Yb2 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.089 Å

Authors

Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.

Funding support

Taiwan, 2items

Citation

Journal: Nat Commun / Year: 2023
Title: Structural insights into the regulation, ligand recognition, and oligomerization of bacterial STING.
Authors: Hou, M.H. / Wang, Y.C. / Yang, C.S. / Liao, K.F. / Chang, J.W. / Shih, O. / Yeh, Y.Q. / Sriramoju, M.K. / Weng, T.W. / Jeng, U.S. / Hsu, S.D. / Chen, Y.

History

Deposition	Jan 7, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 10, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8hyn.cif.gz	89.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8hyn.ent.gz	64.1 KB	Display	PDB format
PDBx/mmJSON format	8hyn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8hyn_validation.pdf.gz	962.3 KB	Display	wwPDB validaton report
Full document	8hyn_full_validation.pdf.gz	964 KB	Display
Data in XML	8hyn_validation.xml.gz	18 KB	Display
Data in CIF	8hyn_validation.cif.gz	26.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hy/8hyn ftp://data.pdbj.org/pub/pdb/validation_reports/hy/8hyn	HTTPS FTP

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Related structure data

Related structure data	8hwiC 8hwjC 8hy8C 8hy9C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CD-NTase-associated protein 12

B: CD-NTase-associated protein 12

hetero molecules

37.5 kDa, 2 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)	53.265, 60.121, 118.823
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	CD-NTase-associated protein 12 / NAD(+) hydrolase / TIR-STING Mass: 18563.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Riemerella anatipestifer Yb2 (bacteria) Gene: KYF39_09390 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A8F6THR5, NAD+ glycohydrolase
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.56 Å³/Da / Density % sol: 51.99 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M Imidazole/MES pH 6.5, 0.1 M carboxylic acids, 20% v/v Ethylene glycol, 10 % w/v PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.089→30 Å / Num. obs: 22890 / % possible obs: 98.3 % / Redundancy: 7.1 % / R_merge(I) obs: 0.042 / Net I/σ(I): 43.126
Reflection shell	Resolution: 2.089→2.18 Å / R_merge(I) obs: 0.301 / Num. unique obs: 2235

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.17.1_3660	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.089→25.957 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.912 / SU B: 4.958 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2387	1140	5.003 %
R_work	0.1893	21648	-
all	0.192	-	-
obs	-	22788	97.643 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 33.11 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.135 Å²	0 Å²	0 Å²
2-	-	0.533 Å²	-0 Å²
3-	-	-	-0.398 Å²

Refinement step

Cycle: LAST / Resolution: 2.089→25.957 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2553	0	26	360	2939

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	2624
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.017	2520
X-RAY DIFFRACTION	r_angle_refined_deg	1.395	1.648	3549
X-RAY DIFFRACTION	r_angle_other_deg	1.438	1.583	5806
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.043	5	313
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.362	24.46	139
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.729	15	465
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.275	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	361
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2939
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	597
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	546
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	2393
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	1325
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	1251
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.222	0.2	238
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.056	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.218	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.257	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.204	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	2.928	3.172	1258
X-RAY DIFFRACTION	r_mcbond_other	2.919	3.17	1257
X-RAY DIFFRACTION	r_mcangle_it	4.29	4.745	1569
X-RAY DIFFRACTION	r_mcangle_other	4.289	4.748	1570
X-RAY DIFFRACTION	r_scbond_it	3.573	3.589	1366
X-RAY DIFFRACTION	r_scbond_other	3.572	3.59	1367
X-RAY DIFFRACTION	r_scangle_it	5.644	5.197	1980
X-RAY DIFFRACTION	r_scangle_other	5.642	5.198	1981
X-RAY DIFFRACTION	r_lrange_it	8.2	38.343	3048
X-RAY DIFFRACTION	r_lrange_other	8.063	37.739	2964

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 (%)
2.089-2.143	0.262	75	0.241	1431	X-RAY DIFFRACTION	89.1124
2.143-2.201	0.255	80	0.215	1508	X-RAY DIFFRACTION	97.3636
2.201-2.265	0.279	78	0.253	1486	X-RAY DIFFRACTION	97.8111
2.265-2.334	0.277	76	0.213	1438	X-RAY DIFFRACTION	97.1135
2.334-2.41	0.305	75	0.203	1428	X-RAY DIFFRACTION	98.4283
2.41-2.494	0.24	72	0.194	1371	X-RAY DIFFRACTION	99.0391
2.494-2.588	0.28	69	0.197	1318	X-RAY DIFFRACTION	97.8138
2.588-2.693	0.256	66	0.185	1261	X-RAY DIFFRACTION	98.0783
2.693-2.811	0.242	66	0.177	1246	X-RAY DIFFRACTION	98.5725
2.811-2.947	0.25	63	0.182	1181	X-RAY DIFFRACTION	99.2817
2.947-3.105	0.23	59	0.194	1127	X-RAY DIFFRACTION	99.2469
3.105-3.291	0.25	56	0.195	1064	X-RAY DIFFRACTION	99.0274
3.291-3.515	0.248	54	0.192	1028	X-RAY DIFFRACTION	98.9936
3.515-3.793	0.171	50	0.173	949	X-RAY DIFFRACTION	98.9109
3.793-4.148	0.169	46	0.153	865	X-RAY DIFFRACTION	99.1295
4.148-4.626	0.211	42	0.147	819	X-RAY DIFFRACTION	99.5376
4.626-5.321	0.201	39	0.157	725	X-RAY DIFFRACTION	99.7389
5.321-6.466	0.363	32	0.262	602	X-RAY DIFFRACTION	97.6888
6.466-8.94	0.222	26	0.209	508	X-RAY DIFFRACTION	99.2565
8.94-25.957	0.282	16	0.168	292	X-RAY DIFFRACTION	91.3947

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