PDB-2wte: The structure of the CRISPR-associated protein, Csa3, from Sulfol...

ID or keywords:

Entry

Database: PDB / ID: 2wte

Title

The structure of the CRISPR-associated protein, Csa3, from Sulfolobus solfataricus at 1.8 angstrom resolution.

Components

CSA3

Keywords

ANTIVIRAL PROTEIN / VIRAL RESISTANCE / WINGED HELIX-TURN-HELIX / RNAI / PRNAI NUCLEOTIDE-BINDING DOMAIN

Function / homology

Function and homology information

defense response to virus / DNA binding
Similarity search - Function

Biological species

SULFOLOBUS SOLFATARICUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Lintner, N.G. / Alsbury, D.L. / Copie, V. / Young, M.J. / Lawrence, C.M.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: The Structure of the Crispr-Associated Protein Csa3 Provides Insight Into the Regulation of the Crispr/Cas System.
Authors: Lintner, N.G. / Frankel, K.A. / Tsutakawa, S.E. / Alsbury, D.L. / Copie, V. / Young, M.J. / Tainer, J.A. / Lawrence, C.M.

History

Deposition	Sep 15, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 22, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wte.cif.gz	186.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2wte.ent.gz	151.7 KB	Display	PDB format
PDBx/mmJSON format	2wte.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wte_validation.pdf.gz	443.8 KB	Display	wwPDB validaton report
Full document	2wte_full_validation.pdf.gz	448.3 KB	Display
Data in XML	2wte_validation.xml.gz	21 KB	Display
Data in CIF	2wte_validation.cif.gz	28.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wt/2wte ftp://data.pdbj.org/pub/pdb/validation_reports/wt/2wte	HTTPS FTP

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Related structure data

Similar structure data	6w11-d 7kx5-1 2d2d-d 6ya0-1 5rgw-1 5rf9-1 7jw8-1 5rg0-1 5rfe-1 7aha-1 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: CSA3

B: CSA3

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.426, 89.853, 102.577
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	CSA3 Mass: 28233.557 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SELENOMETHIONINE-INCORPORATED / Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PDEST14 (INVITROGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-PLYSS / References: UniProt: Q97Y88
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	N-TERMINAL HEXAHISTIDINE TAG ADDED FOR PURIFICATION

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.5 % / Description: NONE
Crystal grow	pH: 7.5 Details: 40% MPD, 5% PEG-8000, 0.1M SODIUM CACODYLATE PH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.91737
Detector	Type: ADSC CCD / Detector: CCD / Date: Dec 11, 2008 Details: VERTICAL FOCUSING MIRROR, SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Radiation	Monochromator: SIDE-SCATTERING CUBEROOT I- BEAM BENT SINGLE CRYSTAL, ASYMETRIC CUT 12.2 DEGS Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91737 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 46357 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4 % / R_merge(I) obs: 0.04 / Net I/σ(I): 27.5
Reflection shell	Resolution: 1.8→1.84 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.3.0036	refinement
DENZO		data reduction
SCALEPACK		data scaling
SOLVE-RESOLVE		phasing

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 1.8→67.57 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.937 / SU B: 4.817 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21994	2367	5.1 %	RANDOM
R_work	0.17967	-	-	-
obs	0.1817	43935	99.5 %	-

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: 16.313 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.5 Å²	0 Å²	0 Å²
2-	-	1.23 Å²	0 Å²
3-	-	-	-0.73 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→67.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3350	0	4	164	3518

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	3450
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2434
X-RAY DIFFRACTION	r_angle_refined_deg	1.287	2.006	4656
X-RAY DIFFRACTION	r_angle_other_deg	0.859	3	5981
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.266	5	435
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.381	23.869	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.526	15	709
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.139	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	567
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3698
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	651
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	778
X-RAY DIFFRACTION	r_nbd_other	0.187	0.2	2500
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	1758
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	1845
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	146
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.153	0.2	14
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.308	0.2	45
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.168	0.2	18
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	3.125	3	2678
X-RAY DIFFRACTION	r_mcbond_other	0.91	3	863
X-RAY DIFFRACTION	r_mcangle_it	3.268	4	3494
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	7.949	12	1434
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	10.319	18	1158
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.329	174	-
R_work	0.234	3202	-
obs	-	-	99.79 %

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	4.1017	2.0483	-0.915	4.3894	-0.5399	6.9088	0.0066	-0.4798	-0.3493	0.1255	-0.0561	0.0351	0.1952	0.0772	0.0495	0.0721	0.0044	-0.0189	0.2278	0.0431	0.189	9.2817	62.1699	74.4506
2	4.2565	-0.1461	-1.7535	2.359	-0.5282	2.1525	-0.009	0.0012	-0.2139	-0.3433	-0.0513	0.0198	0.1994	-0.0076	0.0602	0.1086	0.0199	-0.0208	0.1773	0.0058	0.168	5.7956	61.4952	65.3008
3	4.5996	1.1143	-1.805	2.9114	-1.0855	3.0447	0.0048	-0.0368	-0.2921	0.0129	0.0539	0.048	0.2603	-0.101	-0.0587	0.0964	0.0252	-0.0186	0.1804	-0.0065	0.1579	2.9631	62.2324	67.8429
4	2.7998	1.4567	-0.7628	1.9025	-0.6673	2.393	-0.0209	0.112	0.2531	-0.1238	0.1348	0.1492	-0.0984	-0.2923	-0.1139	0.1123	0.0496	-0.0076	0.1332	-0.0253	0.1677	12.4751	75.538	66.5047
5	2.0378	-0.0477	-0.2763	2.3948	0.5716	2.6845	0.0538	-0.1216	-0.0422	0.0973	-0.0077	-0.0212	0.072	-0.1145	-0.0462	0.0686	0.0027	-0.0125	0.1098	-0.0077	0.1176	18.3349	68.9485	74.0585
6	5.6915	4.0558	0.5999	11.9839	2.998	6.3255	0.3311	-0.055	0.3773	-0.4166	-0.3159	0.1248	-0.5043	-0.0581	-0.0152	0.1897	0.0322	0.0038	0.1665	-0.0427	0.1764	23.8189	83.0276	83.3981
7	4.2961	-0.3561	-1.0947	5.6131	-1.8084	7.9757	-0.2001	-0.3591	0.2494	0.3273	0.4216	-0.8485	-0.3769	0.8941	-0.2215	0.2073	-0.0427	-0.0072	0.2875	-0.1797	0.2196	32.1726	84.8036	97.7636
8	4.5029	-0.4859	-1.833	10.8292	6.2257	9.9551	0.113	0.128	0.5009	0.5704	0.4026	-0.1211	-0.5268	0.2693	-0.5156	0.2715	0.0048	0.1557	0.0947	-0.0432	0.1132	24.0489	88.5204	100.1435
9	3.3766	-1.6988	-2.712	3.4157	1.7769	12.7243	-0.3072	-0.3049	-0.2813	0.6249	0.2273	0.0451	0.6001	0.2307	0.0799	0.2351	0.0194	0.0322	0.1765	-0.0268	0.113	27.2161	77.5148	95.4975
10	3.3642	0.2907	-2.0045	5.6972	-1.0664	6.6158	-0.0017	0.242	-0.033	-0.158	0.05	-0.0425	0.1073	-0.0321	-0.0483	0.0679	0.0313	-0.0084	0.1374	0.0143	0.1536	37.9177	66.6371	62.3236
11	3.3612	0.5601	-1.4962	1.0285	-0.1092	3.1626	-0.0671	-0.0456	-0.2342	0.0764	0.0637	-0.0396	0.4504	0.084	0.0034	0.1264	0.0227	-0.0184	0.1101	0.0122	0.1522	41.7686	60.169	68.7152
12	3.2459	0.4076	-2.4871	2.513	-1.0213	5.6111	0.0463	-0.0822	-0.1843	-0.0599	-0.0005	0.0523	0.1207	0.067	-0.0458	0.0576	0.0171	-0.0211	0.138	0.0202	0.1518	43.8561	63.0579	67.8173
13	3.803	0.6665	-1.2406	1.3817	-0.3853	3.62	0.1228	-0.4417	0.0913	0.1817	-0.0511	0.0246	-0.037	0.2968	-0.0717	0.1125	0.0073	-0.0093	0.1021	-0.027	0.1501	34.5917	72.1858	76.7103
14	2.4249	0.4773	-0.0567	1.9418	-0.2024	2.2345	0.018	0.0092	-0.0153	-0.0783	-0.0294	0.0307	-0.0059	-0.011	0.0114	0.0743	0.0205	-0.0077	0.0723	-0.0131	0.1088	28.7044	71.5922	66.5192
15	10.8398	-6.9796	-3.489	9.948	5.7249	4.2497	-0.0846	-0.5025	0.2361	0.3309	0.2634	-0.5987	-0.0435	0.0394	-0.1788	0.1861	0.0433	-0.0425	0.0952	-0.032	0.1343	23.1973	87.9731	68.0592
16	4.0995	2.6464	4.2504	7.2982	5.0564	13.1781	-0.3517	-0.1412	0.6728	-0.56	-0.0016	0.6167	-0.538	-0.2434	0.3534	0.2547	0.0478	-0.1355	0.0442	0.0102	0.1888	13.3805	97.3708	59.6196
17	4.2457	0.9473	-0.9794	20.2698	2.8456	5.4361	-0.1397	0.1466	0.0047	-1.0965	0.2032	-0.4312	-0.9648	0.3841	-0.0635	0.441	-0.1562	-0.0921	0.0502	0.0538	0.117	21.4938	103.6412	57.3503
18	6.6391	0.2772	0.3966	8.2368	-2.1959	8.0393	-0.0684	0.2524	-0.0383	-0.3976	0.1391	0.3037	-0.4301	-0.076	-0.0707	0.205	0.0515	-0.0612	0.0807	-0.0042	0.0939	16.6879	90.1448	59.3826

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 24
2	X-RAY DIFFRACTION	2	A	25 - 49
3	X-RAY DIFFRACTION	3	A	50 - 68
4	X-RAY DIFFRACTION	4	A	69 - 93
5	X-RAY DIFFRACTION	5	A	94 - 133
6	X-RAY DIFFRACTION	6	A	134 - 143
7	X-RAY DIFFRACTION	7	A	144 - 163
8	X-RAY DIFFRACTION	8	A	164 - 187
9	X-RAY DIFFRACTION	9	A	188 - 212
10	X-RAY DIFFRACTION	10	B	1 - 24
11	X-RAY DIFFRACTION	11	B	25 - 51
12	X-RAY DIFFRACTION	12	B	52 - 68
13	X-RAY DIFFRACTION	13	B	69 - 93
14	X-RAY DIFFRACTION	14	B	94 - 133
15	X-RAY DIFFRACTION	15	B	134 - 143
16	X-RAY DIFFRACTION	16	B	144 - 160
17	X-RAY DIFFRACTION	17	B	161 - 186
18	X-RAY DIFFRACTION	18	B	187 - 215

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