PDB-3ps0: The structure of the CRISPR-associated protein, csa2, from Sulfol...

ID or keywords:

Entry

Database: PDB / ID: 3ps0

Title

The structure of the CRISPR-associated protein, csa2, from Sulfolobus solfataricus

Components

CRISPR-Associated protein, CSA2

Keywords

RNA BINDING PROTEIN / CRISPR-Associated / Viral resistance /

crispr / cas / cass / RNA-Binding / RNA-Recognition motif /

Nucleic-acid binding /

Protein-protein interactions /

RNA-binding protein

Function / homology

CRISPR-associated protein Cas7/Cst2/DevR, subtype I-a/Apern / CRISPR-associated protein Cas7/Cst2/DevR / CRISPR-associated negative auto-regulator DevR/Csa2 / defense response to virus /

RNA binding / CRISPR-associated aCascade subunit Cas7/Csa2 2

Function and homology information

Biological species

Sulfolobus solfataricus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2 Å

Authors

Lintner, N.G. / Sdano, M. / Young, M.J. / Lawrence, C.M.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE).
Authors: Lintner, N.G. / Kerou, M. / Brumfield, S.K. / Graham, S. / Liu, H. / Naismith, J.H. / Sdano, M. / Peng, N. / She, Q. / Copie, V. / Young, M.J. / White, M.F. / Lawrence, C.M.

History

Deposition	Nov 30, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 20, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 14, 2011	Group: Database references
Revision 1.3	Oct 25, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4	Feb 21, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ps0.cif.gz	453 KB	Display	PDBx/mmCIF format
PDB format	pdb3ps0.ent.gz	378.1 KB	Display	PDB format
PDBx/mmJSON format	3ps0.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/ps/3ps0 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/3ps0	HTTPS FTP

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Related structure data

Similar structure data	3mw1-d 3hl7-d 5r9i-d 3u8w-d 3p7c-d 5omh-d 4kiq-4 4u2j-2 1kv2-d 3roc-d 3mvl-1 5r8w-d 4eh7-d 3qbt-2 5o8u-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#181 - Jan 2015 Cascade and CRISPR similarity (2)

Deposited unit

A: CRISPR-Associated protein, CSA2

B: CRISPR-Associated protein, CSA2

C: CRISPR-Associated protein, CSA2

D: CRISPR-Associated protein, CSA2

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

1

A: CRISPR-Associated protein, CSA2

defined by author
Evidence: equilibrium centrifugation
36.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: CRISPR-Associated protein, CSA2

defined by author
Evidence: equilibrium centrifugation
36.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: CRISPR-Associated protein, CSA2

defined by author
Evidence: equilibrium centrifugation
36.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: CRISPR-Associated protein, CSA2

defined by author
Evidence: equilibrium centrifugation
36.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.642, 120.876, 158.056
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

The biological assembly is experimentally determined using analytical ultracentrifugation as monomer.

#1: Protein	CRISPR-Associated protein, CSA2 Mass: 36268.574 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: SSO1442 / Plasmid: PDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q97Y91
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.46 Å³/Da / Density % sol: 49.95 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 2.0 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.0, 0.2 M SODIUM THIOCYANATE, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.95369, 1.04013, 1.03982, 0.96109

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 24, 2009
Details: FLAT COLLIMATING MIRROR, DOUBLE CRYSTAL MONOCHROMATOR, TOROID FOCUSING MIRROR

Radiation

Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.95369	1
2	1.04013	1
3	1.03982	1
4	0.96109	1

Reflection

Resolution: 2→90 Å / Num. obs: 96002 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / R_merge(I) obs: 0.041 / Net I/σ(I): 34.6

Reflection shell

Resolution: 2→2.05 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.457 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software

Name	Version	Classification
SOLVE		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2→33.75 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.947 / SU B: 6.659 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.221	4790	5 %	RANDOM
R_work	0.183	-	-	-
obs	0.185	91161	98.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 45.841 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.63 Å²	0 Å²	0 Å²
2-	-	-0.16 Å²	0 Å²
3-	-	-	-0.47 Å²

Refinement step

Cycle: LAST / Resolution: 2→33.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8776	0	0	545	9321

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	8942
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	6152
X-RAY DIFFRACTION	r_angle_refined_deg	0.93	1.986	12052
X-RAY DIFFRACTION	r_angle_other_deg	0.744	3	15073
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.312	5	1116
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.222	24.022	363
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.719	15	1642
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.601	15	50
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	1397
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	9710
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1728
X-RAY DIFFRACTION	r_nbd_refined	0.188	0.2	1710
X-RAY DIFFRACTION	r_nbd_other	0.185	0.2	6271
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	4385
X-RAY DIFFRACTION	r_nbtor_other	0.081	0.2	4548
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.125	0.2	471
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.012	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.181	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.196	0.2	57
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.128	0.2	34
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	4.693	4.5	7282
X-RAY DIFFRACTION	r_mcbond_other	0.925	4.5	2292
X-RAY DIFFRACTION	r_mcangle_it	3.905	6	9029
X-RAY DIFFRACTION	r_scbond_it	9.168	15	3857
X-RAY DIFFRACTION	r_scangle_it	11.665	22.5	3020
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.246	354	-
R_work	0.2	6697	-
obs	-	-	99.46 %

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	1.6708	-0.7762	0.3905	1.9231	-0.6512	2.8254	-0.3187	0.1272	-0.0091	-0.2941	-0.0347	-0.019	0.0657	0.065	0.3534	0.1723	-0.0109	-0.0392	0.1125	0.0069	0.0994	106.9874	72.8047	79.973
2	4.5	0.1992	2.065	0.249	-0.3707	2.6219	0.0377	-0.1591	-0.2641	-0.1411	0.0022	0.0929	0.0488	-0.2419	-0.04	0.1727	-0.0003	-0.0769	0.1651	0.0022	0.1648	101.0999	68.5072	82.8653
3	2.3923	-0.0612	0.3811	2.5898	-0.9667	3.1903	-0.038	0.1053	-0.2043	-0.2278	-0.0254	0.1508	0.5158	0.1347	0.0633	0.1602	-0.0093	0.0413	0.1824	0.0176	0.1375	121.5886	57.0803	100.1406
4	1.0154	-0.3632	1.2221	0.1386	-0.5212	2.2807	-0.0788	-0.1407	0.002	-0.0801	0.0011	0.0384	-0.0278	-0.2455	0.0777	0.1637	-0.0167	-0.0458	0.2012	-0.0023	0.1777	106.5194	68.7344	88.7091
5	2.3114	-0.5917	1.2892	1.8755	0.2229	1.7709	-0.1458	-0.2124	0.1337	0.0486	-0.0831	0.0396	-0.1975	-0.0669	0.2289	0.0682	-0.0129	-0.0252	0.2089	0.004	0.1283	120.747	70.8361	106.7042
6	1.4283	1.2856	0.8628	1.2939	-0.0735	5.807	-0.4345	-0.1614	0.1114	-0.0556	0.1576	0.0336	-0.2399	-0.0145	0.2769	0.2059	0.0844	-0.1131	0.1077	0.0216	0.1166	106.664	80.8965	87.0943
7	2.3216	0.5768	-0.7995	2.3135	-0.5206	5.514	-0.0923	-0.3259	0.6148	0.0994	0.0851	0.1206	-1.1133	-0.2529	0.0073	0.3364	0.0514	-0.1851	0.0814	-0.0508	0.1894	107.9884	89.0373	92.6871
8	2.7485	-0.6396	1.782	3.0975	-0.5579	1.5936	-0.0328	-0.2051	-0.2344	0.4709	-0.0034	-0.0191	0.0373	-0.2054	0.0361	0.1953	0.016	-0.0227	0.0964	-0.0009	0.2023	80.0935	76.0583	129.29
9	3.4945	-0.7062	1.1972	0.3524	-0.2392	1.3861	0.1062	-0.0759	-0.1009	0.1986	-0.0836	-0.1442	-0.0361	0.0749	-0.0226	0.1611	-0.0329	-0.1042	0.085	0.0367	0.2166	87.0779	69.4925	130.7824
10	1.4134	0.3521	0.2825	2.8868	0.1933	1.7865	-0.0848	0.0742	-0.192	-0.0384	0.054	-0.0307	0.206	-0.1263	0.0307	0.108	-0.0092	-0.0088	0.1426	0.0044	0.1638	66.7631	62.3086	112.285
11	1.3555	-0.2477	1.2916	0.2621	-0.6388	2.787	0.0457	-0.1554	-0.1425	0.2047	-0.0014	-0.1329	-0.1308	0.0692	-0.0443	0.2114	-0.0223	-0.1113	0.124	0.0292	0.215	87.9107	75.4291	133.8549
12	1.9841	0.3688	0.1993	2.3915	0.1574	1.4178	-0.0589	0.2885	0.058	-0.2397	0.0798	0.0582	0.0168	-0.1555	-0.0209	0.1259	0.0034	-0.0176	0.1757	0.0318	0.139	66.3894	74.148	106.3336
13	1.8672	-0.5815	0.7667	2.0701	-0.7489	3.1983	0.0561	0.0759	0.0384	0.2556	-0.0886	-0.2519	-0.1696	0.1495	0.0325	0.1539	-0.0075	-0.0605	0.0374	-0.0038	0.1671	83.275	86.5318	122.801
14	3.6549	-0.0455	2.7224	2.8293	0.2779	5.8952	-0.2012	-0.0413	0.2677	0.3354	0.0852	-0.2182	-0.4939	0.0147	0.1159	0.241	0.0356	-0.0082	0.0428	-0.0014	0.1733	76.1005	92.0475	125.1206
15	1.3936	0.3087	-0.6477	1.7929	0.3684	3.214	-0.0861	-0.1549	0.0681	0.465	-0.1253	-0.1429	0.024	-0.2545	0.2114	0.1067	0.002	-0.0049	0.272	-0.0398	0.1335	90.0779	62.6638	86.1102
16	2.3926	-1.5523	-0.0147	1.7966	0.6271	1.6735	-0.1137	-0.2777	0.0029	0.1705	0.2376	-0.1532	0.4667	0.2104	-0.1239	0.3671	0.0371	-0.0383	0.2028	0.0251	0.1728	107.8596	47.3911	90.0573
17	5.8996	-0.6115	-2.5348	2.4177	1.3258	5.2758	0.0275	0.5924	0.1015	-0.0067	0.2218	-0.3115	0.4022	0.4393	-0.2493	0.3316	0.0949	-0.026	0.2863	-0.046	0.1832	112.9551	43.646	78.2598
18	2.6144	-1.0291	0.3383	2.0772	0.9764	2.8498	-0.1108	0.1347	-0.111	0.2364	-0.1718	0.1081	0.4117	-0.3248	0.2827	0.2206	-0.0966	0.0553	0.198	-0.0203	0.1542	91.7824	52.7408	83.6058
19	3.1423	-0.6533	0.4144	0.8249	0.5993	2.0939	-0.1199	-0.1386	-0.5107	0.314	0.0357	0.099	0.7324	-0.1292	0.0842	0.3743	-0.1082	0.1314	0.0641	0.0101	0.1679	95.4021	41.3973	83.2412
20	2.1691	0.1332	1.1128	2.3284	1.3414	6.2904	-0.1807	-0.1449	0.0103	0.0725	-0.2691	0.1524	0.2629	-0.9726	0.4499	0.0697	-0.209	0.1445	0.312	-0.1642	0.127	78.3472	49.1238	77.6523
21	2.0406	-0.0031	-3.1187	2.7135	1.6516	5.7659	0.0893	-0.7543	-0.9789	-0.1466	-0.4305	1.1601	0.4446	-1.0835	0.3412	0.4553	-0.221	0.0748	0.4324	-0.1072	0.3747	77.8709	44.2252	88.8808
22	0.9833	0.1934	-0.1425	1.2467	0.3277	1.1429	-0.1284	0.1064	0.2183	-0.2627	-0.0735	0.004	-0.2753	0.2059	0.202	0.1009	-0.0671	-0.0454	0.1678	0.0925	0.18	98.9264	64.2142	127.9375
23	0.6985	0.4143	0.2803	1.4668	-0.3527	0.953	-0.0599	0.0417	0.0562	0.0232	0.0317	0.0882	-0.0385	-0.122	0.0283	0.1345	-0.0149	-0.0117	0.1209	0.0115	0.1678	76.9479	50.4718	123.9314
24	1.2237	0.7101	-0.2685	1.4636	-0.6799	1.3507	0.0191	-0.1101	0.082	0.1533	-0.1044	0.0105	-0.1336	-0.0242	0.0853	0.1552	0.0004	-0.0019	0.1288	-0.0079	0.1756	82.1495	51.7051	131.5152
25	1.0038	0.7629	0.4663	1.8808	0.0538	1.3048	-0.0243	-0.0375	-0.0757	0.0887	-0.0437	-0.0524	0.1435	-0.0348	0.068	0.1385	-0.0058	0.0194	0.117	0.0117	0.1514	82.9258	39.5205	132.5298
26	2.0546	0.9893	-0.935	2.9891	-1.3977	4.4821	-0.1856	0.2086	0.1386	-0.3066	0.1369	0.0137	0.0753	0.0848	0.0486	0.0487	-0.0005	0.0371	0.1655	0.0523	0.1744	99.3302	48.6124	126.2284
27	1.4987	0.0722	0.2189	1.8751	-1.0419	3.6283	-0.1754	-0.1597	0.1326	0.1768	-0.0647	-0.2267	-0.07	0.7355	0.2401	0.0206	0.0238	0.0285	0.2225	0.0826	0.1411	105.9953	47.3085	136.058
28	4.9345	0.7731	-0.3457	4.986	-1.5232	5.4463	-0.198	0.1657	-0.421	-0.1388	-0.11	-0.4419	0.3599	0.8853	0.308	0.0245	0.0961	0.1283	0.2021	0.0605	0.0944	105.5029	41.5261	124.3161

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 29
2	X-RAY DIFFRACTION	2	A	30 - 64
3	X-RAY DIFFRACTION	3	A	65 - 105
4	X-RAY DIFFRACTION	4	A	106 - 192
5	X-RAY DIFFRACTION	5	A	193 - 226
6	X-RAY DIFFRACTION	6	A	227 - 272
7	X-RAY DIFFRACTION	7	A	273 - 320
8	X-RAY DIFFRACTION	8	C	1 - 28
9	X-RAY DIFFRACTION	9	C	29 - 63
10	X-RAY DIFFRACTION	10	C	64 - 135
11	X-RAY DIFFRACTION	11	C	136 - 193
12	X-RAY DIFFRACTION	12	C	194 - 225
13	X-RAY DIFFRACTION	13	C	226 - 296
14	X-RAY DIFFRACTION	14	C	297 - 321
15	X-RAY DIFFRACTION	15	B	1 - 44
16	X-RAY DIFFRACTION	16	B	45 - 98
17	X-RAY DIFFRACTION	17	B	99 - 132
18	X-RAY DIFFRACTION	18	B	133 - 198
19	X-RAY DIFFRACTION	19	B	199 - 260
20	X-RAY DIFFRACTION	20	B	261 - 295
21	X-RAY DIFFRACTION	21	B	296 - 319
22	X-RAY DIFFRACTION	22	D	1 - 42
23	X-RAY DIFFRACTION	23	D	43 - 99
24	X-RAY DIFFRACTION	24	D	100 - 185
25	X-RAY DIFFRACTION	25	D	186 - 228
26	X-RAY DIFFRACTION	26	D	229 - 259
27	X-RAY DIFFRACTION	27	D	260 - 295
28	X-RAY DIFFRACTION	28	D	296 - 320

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi