PDB-7pqa: Crystal Structure of the Ring Nuclease 0811 mutant-S12G/K169G fro...

ID or keywords:

Entry

Database: PDB / ID: 7pqa

Title

Crystal Structure of the Ring Nuclease 0811 mutant-S12G/K169G from Sulfolobus islandicus (Sis0811)

Components

CRISPR-associated protein, APE2256 family

Keywords

ANTIVIRAL PROTEIN / RING NUCLEASE / CRISPR-ASSOCIATED PROTEIN /

HELIX-TURN-HELIX / VIRAL RESISTANCE / CARF NUCLEOTIDE-BINDING DOMAIN / CRISPR Ring Nuclease

Function / homology

CRISPR system ring nuclease SSO1393 / CRISPR system ring nuclease SSO1393-like / CRISPR-associated protein (Cas_APE2256) / CRISPR-associated protein, APE2256 family

Function and homology information

Biological species

Sulfolobus islandicus REY15A (acidophilic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

Molina, R. / Jensen, A.L.G. / Marchena-Hurtado, J. / Lopez-Mendez, B. / Stella, S. / Montoya, G.

Funding support

Denmark, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2021
Title: Structural basis of cyclic oligoadenylate degradation by ancillary Type III CRISPR-Cas ring nucleases.
Authors: Molina, R. / Jensen, A.L.G. / Marchena-Hurtado, J. / Lopez-Mendez, B. / Stella, S. / Montoya, G.

History

Deposition	Sep 16, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 1, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 15, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Nov 22, 2023	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / struct_keywords / struct_ncs_dom_lim Item: _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3	Jan 31, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7pqa.cif.gz	213.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pq/7pqa ftp://data.pdbj.org/pub/pdb/validation_reports/pq/7pqa	HTTPS FTP

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Related structure data

Related structure data	7pq2SC 7pq3C 7pq6C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7pq2-d 7pq6-d 3tqt-d 3mt5-d 4eze-d 4osj-2 4pbv-1 6vw8-2 3naf-d 3cnv-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: CRISPR-associated protein, APE2256 family

BBB: CRISPR-associated protein, APE2256 family

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

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	76.930, 104.970, 78.306
Angle α, β, γ (deg.)	90.000, 102.890, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 1 / Auth seq-ID: 1 - 267 / Label seq-ID: 1 - 267

Dom-ID	Auth asym-ID	Label asym-ID
1	AAA	A
2	BBB	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	CRISPR-associated protein, APE2256 family Mass: 31551.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus islandicus REY15A (acidophilic) Gene: SiRe_0811 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F0NH89
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.1M Bis-Tris propane pH 7.5, 0.2M KSCN

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9779 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9779 Å / Relative weight: 1
Reflection	Resolution: 2.04→76.38 Å / Num. obs: 38798 / % possible obs: 97.6 % / Redundancy: 7.1 % / CC_1/2: 0.99 / Net I/σ(I): 18.5
Reflection shell	Resolution: 2.04→2.07 Å / Num. unique obs: 1925 / CC_1/2: 0.839

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7PQ2

7pq2

Resolution: 2.04→43.932 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.943 / SU B: 11.707 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.199 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2379	1913	5.002 %
R_work	0.1942	36331	-
all	0.196	-	-
obs	-	38244	99.096 %

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: 53.097 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.007 Å²	-0 Å²	-0.514 Å²
2-	-	0.614 Å²	0 Å²
3-	-	-	-0.349 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→43.932 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4398	0	0	77	4475

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	4479
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4365
X-RAY DIFFRACTION	r_angle_refined_deg	1.86	1.639	6040
X-RAY DIFFRACTION	r_angle_other_deg	1.431	1.585	10097
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.326	5	541
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.476	23.973	224
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.624	15	860
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.626	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	566
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	4938
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	962
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	929
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	3934
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	2222
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	2247
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.186	0.2	113
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.104	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.224	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.221	0.2	53
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.181	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	3.397	4.09	2170
X-RAY DIFFRACTION	r_mcbond_other	3.397	4.089	2169
X-RAY DIFFRACTION	r_mcangle_it	5.123	6.12	2709
X-RAY DIFFRACTION	r_mcangle_other	5.122	6.12	2710
X-RAY DIFFRACTION	r_scbond_it	3.962	4.552	2308
X-RAY DIFFRACTION	r_scbond_other	3.961	4.552	2309
X-RAY DIFFRACTION	r_scangle_it	6.2	6.628	3330
X-RAY DIFFRACTION	r_scangle_other	6.199	6.629	3331
X-RAY DIFFRACTION	r_lrange_it	8.777	47.82	5057
X-RAY DIFFRACTION	r_lrange_other	8.777	47.801	5053
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.157	0.05	8059

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.15665	0.05006
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.15665	0.05006

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.04-2.093	0.312	141	0.295	2672	0.296	2840	0.764	0.775	99.0493	0.285
2.093-2.15	0.289	137	0.269	2594	0.27	2756	0.823	0.84	99.0929	0.251
2.15-2.212	0.321	133	0.243	2535	0.247	2686	0.817	0.872	99.3299	0.223
2.212-2.28	0.287	128	0.23	2427	0.232	2597	0.877	0.895	98.3827	0.206
2.28-2.355	0.216	125	0.209	2388	0.209	2550	0.918	0.922	98.549	0.188
2.355-2.437	0.268	123	0.212	2335	0.215	2465	0.897	0.907	99.716	0.186
2.437-2.529	0.251	118	0.21	2229	0.212	2357	0.909	0.917	99.5757	0.184
2.529-2.632	0.29	113	0.208	2163	0.212	2290	0.903	0.923	99.3886	0.187
2.632-2.748	0.254	109	0.215	2062	0.217	2185	0.907	0.92	99.3593	0.19
2.748-2.882	0.27	103	0.201	1958	0.204	2076	0.904	0.926	99.2775	0.18
2.882-3.037	0.245	98	0.191	1870	0.194	1994	0.917	0.936	98.6961	0.176
3.037-3.22	0.215	94	0.189	1769	0.191	1891	0.937	0.942	98.5193	0.178
3.22-3.441	0.302	87	0.212	1666	0.216	1787	0.881	0.928	98.0974	0.207
3.441-3.715	0.23	82	0.201	1556	0.203	1639	0.938	0.939	99.939	0.199
3.715-4.067	0.222	77	0.17	1464	0.172	1542	0.931	0.952	99.9352	0.177
4.067-4.542	0.18	69	0.166	1298	0.166	1369	0.952	0.96	99.8539	0.182
4.542-5.235	0.203	61	0.166	1169	0.168	1234	0.95	0.961	99.6758	0.183
5.235-6.389	0.324	51	0.211	961	0.217	1044	0.933	0.95	96.9349	0.235
6.389-8.941	0.185	40	0.178	761	0.178	808	0.969	0.962	99.1337	0.207
8.941-43.932	0.19	24	0.158	454	0.16	479	0.969	0.973	99.7912	0.195

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	0.781	-0.2771	0.3892	0.1056	-0.1737	0.508	-0.1042	-0.059	-0.0237	0.0299	0.0323	-0.0188	-0.084	-0.1312	0.0719	0.1009	0.0269	0.0183	0.0384	-0.0212	0.1565	-31.4724	-11.4438	13.2054
2	0.1573	-0.2193	0.2403	0.3382	-0.4005	1.5834	0.0339	0.0028	0.0398	0.0188	-0.0053	-0.0377	-0.1632	0.0094	-0.0286	0.1479	-0.0018	0.0262	0.0013	-0.0135	0.171	-16.0011	-19.2731	27.5276

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	1 - 275
2	X-RAY DIFFRACTION	2	ALL	BBB	1 - 268

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