PDB-8htw: Crystal Structure of the ring nuclease Sso2081 Y133F mutant from ...

ID or keywords:

Entry

Database: PDB / ID: 8htw

Title

Crystal Structure of the ring nuclease Sso2081 Y133F mutant from Saccharolobus solfataricus in its apo form

Components

CRISPR system ring nuclease SSO2081

Keywords

HYDROLASE / Sso2081 / ring nuclease / mutant / Y133F

Function / homology

CRISPR-assoc protein, NE0113/Csx13 / CRISPR-associated protein NE0113 (Cas_NE0113) / Restriction endonuclease type II-like / Lyases; Phosphorus-oxygen lyases / defense response to virus / lyase activity / cytoplasm / CRISPR system ring nuclease SSO2081

Function and homology information

Biological species

Saccharolobus solfataricus P2 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Lin, Z. / Du, L. / Luo, Z.

Funding support

China, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2023
Title: Molecular basis of stepwise cyclic tetra-adenylate cleavage by the type III CRISPR ring nuclease Crn1/Sso2081.
Authors: Du, L. / Zhang, D. / Luo, Z. / Lin, Z.

History

Deposition	Dec 21, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	Mar 8, 2023	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Mar 29, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 16, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	8htw_validation.pdf.gz	428.2 KB	Display	wwPDB validaton report
Full document	8htw_full_validation.pdf.gz	429.7 KB	Display
Data in XML	8htw_validation.xml.gz	14.6 KB	Display
Data in CIF	8htw_validation.cif.gz	19.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ht/8htw ftp://data.pdbj.org/pub/pdb/validation_reports/ht/8htw	HTTPS FTP

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Related structure data

Related structure data	7yghC 7yglC 7yhlSC S: Starting model for refinement C: citing same article (ref.)
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	#8 - Aug 2000 Restriction Enzymes similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #180 - Dec 2014 TAL Effectors similarity (1)

Deposited unit

A: CRISPR system ring nuclease SSO2081

B: CRISPR system ring nuclease SSO2081

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

1

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

Unit cell

Length a, b, c (Å)	43.747, 95.253, 45.836
Angle α, β, γ (deg.)	90.000, 107.803, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	CRISPR system ring nuclease SSO2081 Mass: 20538.842 Da / Num. of mol.: 2 / Mutation: Y133F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO2081 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta References: UniProt: Q7LYJ6, Lyases; Phosphorus-oxygen lyases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H₂O
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: 2.23 Å³/Da / Density % sol: 44.88 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion Details: 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 24137 / % possible obs: 97.6 % / Redundancy: 4.7 % / R_merge(I) obs: 0.086 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2→2.05 Å / R_merge(I) obs: 1.183 / Num. unique obs: 1778

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
HKL-2000		data scaling
MOLREP		phasing
PHENIX		model building
Coot		model building
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7YHL

7yhl

Resolution: 2→47.626 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.939 / SU B: 6.784 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2556	1177	4.881 %
R_work	0.2241	22937	-
all	0.226	-	-
obs	-	24114	99.76 %

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: 49.345 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.979 Å²	0 Å²	1.075 Å²
2-	-	0.663 Å²	0 Å²
3-	-	-	-2.762 Å²

Refinement step

Cycle: LAST / Resolution: 2→47.626 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2849	0	0	62	2911

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	2889
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	2820
X-RAY DIFFRACTION	r_angle_refined_deg	1.6	1.644	3879
X-RAY DIFFRACTION	r_angle_other_deg	0.505	1.565	6595
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.701	5	357
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.703	5	21
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.364	10	589
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.335	10	125
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	445
X-RAY DIFFRACTION	r_chiral_restr_other	0.037	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3199
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	517
X-RAY DIFFRACTION	r_nbd_refined	0.174	0.2	479
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	2593
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	1404
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	1574
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	93
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.13	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.205	0.2	47
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.211	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	5.225	4.62	1434
X-RAY DIFFRACTION	r_mcbond_other	5.224	4.62	1434
X-RAY DIFFRACTION	r_mcangle_it	6.889	6.92	1789
X-RAY DIFFRACTION	r_mcangle_other	6.887	6.921	1790
X-RAY DIFFRACTION	r_scbond_it	6.798	5.478	1455
X-RAY DIFFRACTION	r_scbond_other	6.797	5.476	1454
X-RAY DIFFRACTION	r_scangle_it	9.65	7.876	2090
X-RAY DIFFRACTION	r_scangle_other	9.647	7.877	2091
X-RAY DIFFRACTION	r_lrange_it	11.68	92.243	11497
X-RAY DIFFRACTION	r_lrange_other	11.681	92.246	11492

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
2-2.052	0.378	77	0.365	1698	0.365	1775	0.891	0.9	100	0.352
2.052-2.108	0.367	68	0.333	1673	0.334	1741	0.892	0.918	100	0.312
2.108-2.169	0.332	70	0.301	1610	0.302	1681	0.919	0.934	99.9405	0.279
2.169-2.236	0.336	89	0.276	1526	0.279	1619	0.925	0.945	99.7529	0.252
2.236-2.309	0.29	77	0.265	1545	0.266	1623	0.939	0.952	99.9384	0.243
2.309-2.39	0.352	64	0.282	1447	0.285	1513	0.907	0.951	99.8678	0.256
2.39-2.48	0.359	80	0.266	1378	0.272	1460	0.931	0.955	99.863	0.243
2.48-2.581	0.315	58	0.261	1403	0.263	1463	0.945	0.958	99.8633	0.236
2.581-2.695	0.374	86	0.259	1287	0.266	1374	0.918	0.96	99.9272	0.235
2.695-2.826	0.296	76	0.259	1207	0.261	1285	0.951	0.959	99.8444	0.242
2.826-2.979	0.336	46	0.264	1201	0.267	1251	0.918	0.957	99.6803	0.249
2.979-3.158	0.289	62	0.249	1126	0.251	1194	0.941	0.962	99.4975	0.244
3.158-3.375	0.233	56	0.228	1054	0.228	1115	0.964	0.969	99.5516	0.229
3.375-3.644	0.254	66	0.215	968	0.218	1037	0.962	0.971	99.7107	0.224
3.644-3.99	0.216	58	0.195	890	0.196	955	0.969	0.976	99.267	0.207
3.99-4.457	0.189	50	0.164	809	0.166	861	0.979	0.983	99.7677	0.191
4.457-5.139	0.184	32	0.154	727	0.155	762	0.976	0.987	99.6063	0.186
5.139-6.276	0.205	20	0.206	629	0.206	656	0.987	0.979	98.9329	0.242
6.276-8.799	0.189	28	0.175	489	0.176	517	0.982	0.984	100	0.222
8.799-47.626	0.132	14	0.173	270	0.171	290	0.978	0.979	97.931	0.226

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