PDB-7z56: Crystal Structure of the Ring Nuclease 0455 from Sulfolobus islan...

ID or keywords:

Entry

Database: PDB / ID: 7z56

Title

Crystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in its apo form

Components

CRISPR-associated protein

Keywords

ANTIVIRAL PROTEIN / RING NUCLEASE / CRISPR-ASSOCIATED PROTEIN / VIRAL RESISTANCE / CARF NUCLEOTIDE-BINDING DOMAIN / CRISPR Ring Nuclease

Function / homology

CRISPR-assoc protein, NE0113/Csx13 / CRISPR-associated protein NE0113 (Cas_NE0113) / CRISPR-associated protein

Function and homology information

Biological species

Sulfolobus islandicus REY15A (acidophilic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.27 Å

Authors

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

Funding support

Denmark, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2022
Title: Molecular basis of cyclic tetra-oligoadenylate processing by small standalone CRISPR-Cas ring nucleases.
Authors: Molina, R. / Garcia-Martin, R. / Lopez-Mendez, B. / Jensen, A.L.G. / Ciges-Tomas, J.R. / Marchena-Hurtado, J. / Stella, S. / Montoya, G.

History

Deposition	Mar 8, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 23, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Structure summary / Category: chem_comp_atom / chem_comp_bond / struct_keywords / Item: _struct_keywords.text
Revision 1.2	Jan 31, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7z56.cif.gz	146.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7z56.ent.gz		Display	PDB format
PDBx/mmJSON format	7z56.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7z56_validation.pdf.gz	444.3 KB	Display	wwPDB validaton report
Full document	7z56_full_validation.pdf.gz	449.3 KB	Display
Data in XML	7z56_validation.xml.gz	15.1 KB	Display
Data in CIF	7z56_validation.cif.gz	20 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z5/7z56 ftp://data.pdbj.org/pub/pdb/validation_reports/z5/7z56	HTTPS FTP

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Related structure data

Related structure data	7z55SC S: Starting model for refinement 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

AAA: CRISPR-associated protein

BBB: CRISPR-associated protein

47.3 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)	42.423, 51.000, 80.353
Angle α, β, γ (deg.)	90.000, 98.696, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	CRISPR-associated protein Mass: 23629.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus islandicus REY15A (acidophilic) Gene: SiRe_0455 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F0NGX6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.83 Å³/Da / Density % sol: 32.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22% PEG 4000 0.05 M Tricine pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.91→79.43 Å / Num. obs: 19381 / % possible obs: 85.2 % / Redundancy: 6.3 % / CC_1/2: 0.995 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.91→2.05 Å / Num. unique obs: 970 / CC_1/2: 0.191

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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: 7Z55

7z55

Resolution: 2.27→79.429 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.934 / SU B: 17.659 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / ESU R: 0.385 / ESU R Free: 0.258
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2534	776	4.932 %
R_work	0.1815	14957	-
all	0.185	-	-
obs	-	15733	98.801 %

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: 54.421 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.316 Å²	-0 Å²	-0.287 Å²
2-	-	-0.496 Å²	-0 Å²
3-	-	-	0.256 Å²

Refinement step

Cycle: LAST / Resolution: 2.27→79.429 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2851	0	0	30	2881

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	2892
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2906
X-RAY DIFFRACTION	r_angle_refined_deg	1.829	1.642	3901
X-RAY DIFFRACTION	r_angle_other_deg	1.373	1.586	6715
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.328	5	359
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.738	24.173	139
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.646	15	572
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.807	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	409
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3192
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	592
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	588
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	2842
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	1424
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1656
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	67
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.178	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.202	0.2	80
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.193	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	3.157	4.369	1442
X-RAY DIFFRACTION	r_mcbond_other	3.146	4.367	1441
X-RAY DIFFRACTION	r_mcangle_it	4.63	6.544	1799
X-RAY DIFFRACTION	r_mcangle_other	4.629	6.548	1800
X-RAY DIFFRACTION	r_scbond_it	4.11	5.129	1450
X-RAY DIFFRACTION	r_scbond_other	4.109	5.132	1451
X-RAY DIFFRACTION	r_scangle_it	6.796	7.422	2102
X-RAY DIFFRACTION	r_scangle_other	6.794	7.425	2103
X-RAY DIFFRACTION	r_lrange_it	8.955	52.467	3131
X-RAY DIFFRACTION	r_lrange_other	8.953	52.485	3130

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
2.27-2.329	0.315	49	0.257	1074	0.259	1185	0.819	0.846	94.7679	0.238
2.329-2.393	0.252	53	0.212	1036	0.214	1109	0.885	0.89	98.1966	0.194
2.393-2.462	0.298	57	0.205	1071	0.21	1140	0.857	0.902	98.9474	0.188
2.462-2.538	0.252	66	0.196	1007	0.2	1078	0.895	0.912	99.5362	0.18
2.538-2.621	0.271	46	0.184	971	0.187	1022	0.885	0.922	99.5108	0.175
2.621-2.713	0.248	34	0.196	961	0.198	1000	0.886	0.908	99.5	0.181
2.713-2.815	0.321	53	0.209	935	0.215	993	0.864	0.895	99.4965	0.193
2.815-2.93	0.287	51	0.194	856	0.198	915	0.863	0.916	99.1257	0.181
2.93-3.06	0.272	52	0.189	851	0.194	918	0.91	0.926	98.366	0.182
3.06-3.209	0.241	48	0.176	815	0.179	867	0.915	0.936	99.5386	0.17
3.209-3.382	0.261	39	0.182	764	0.185	806	0.899	0.938	99.6278	0.181
3.382-3.587	0.245	46	0.172	732	0.176	782	0.884	0.944	99.4885	0.178
3.587-3.834	0.229	28	0.175	709	0.177	738	0.913	0.942	99.8645	0.186
3.834-4.14	0.29	30	0.168	651	0.173	686	0.922	0.946	99.2711	0.19
4.14-4.534	0.2	32	0.163	575	0.165	625	0.957	0.958	97.12	0.188
4.534-5.067	0.207	27	0.158	545	0.16	573	0.955	0.96	99.8255	0.181
5.067-5.847	0.262	22	0.177	480	0.181	505	0.922	0.95	99.4059	0.207
5.847-7.152	0.29	17	0.201	421	0.204	442	0.913	0.941	99.095	0.235
7.152-10.073	0.249	18	0.157	310	0.161	339	0.943	0.972	96.7552	0.185
10.073-79.429	0.238	8	0.214	193	0.215	201	0.976	0.96	100	0.265

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	0.7658	0.0556	0.7939	0.3845	0.0309	2.2083	0.0825	0.0015	0.0268	0.0234	-0.0539	0.0135	0.1242	-0.1162	-0.0286	0.0113	-0.001	-0.0009	0.1495	-0.0027	0.0256	18.857	-7.958	8.33
2	1.1444	-0.0634	-0.3153	0.3338	0.4386	3.9059	0.0296	-0.0911	0.0395	0.0362	-0.0672	-0.0026	-0.133	-0.0006	0.0376	0.0265	-0.0309	0.0008	0.1052	-0.0189	0.0057	30.086	0.947	35.616

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	2 - 179
2	X-RAY DIFFRACTION	2	ALL	BBB	2 - 184

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