PDB-6ae1: Crystal structure of Csm2 of the type III-A CRISPR-Cas effector c...

ID or keywords:

Entry

Database: PDB / ID: 6ae1

Title

Crystal structure of Csm2 of the type III-A CRISPR-Cas effector complex

Components

CRISPR-associated protein, TM1810 family

Keywords

RNA BINDING PROTEIN / CRISPR-Cas / Cas protein / crRNA / Csm complex

Function / homology

CRISPR-associated protein, Csm2 Type III-A / Csm2 Type III-A / defense response to virus / RNA binding / CRISPR system Cms protein Csm2

Function and homology information

Biological species

Staphylococcus epidermidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.405 Å

Authors

Numata, T.

Funding support

Japan, 1items

Citation

Journal: J. Mol. Biol. / Year: 2019
Title: Crystal Structures of Csm2 and Csm3 in the Type III-A CRISPR-Cas Effector Complex.
Authors: Takeshita, D. / Sato, M. / Inanaga, H. / Numata, T.

History

Deposition	Aug 3, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 23, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 30, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Feb 27, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	6ae1_validation.pdf.gz	428.8 KB	Display	wwPDB validaton report
Full document	6ae1_full_validation.pdf.gz	429.5 KB	Display
Data in XML	6ae1_validation.xml.gz	9.4 KB	Display
Data in CIF	6ae1_validation.cif.gz	12 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ae/6ae1 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/6ae1	HTTPS FTP

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Related structure data

Related structure data	6ae2C C: citing same article (ref.)
Similar structure data	1rbi-d 1j81-d 1rbf-d 5h0w-d 1fev-d 1j82-d 1j7z-d 2rln-d 4ot4-2 1rbh-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) 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	#181 - Jan 2015 Cascade and CRISPR similarity (1)

Deposited unit

A: CRISPR-associated protein, TM1810 family

B: CRISPR-associated protein, TM1810 family

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

1

A: CRISPR-associated protein, TM1810 family

defined by author
Evidence: gel filtration
17.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: CRISPR-associated protein, TM1810 family

defined by author
17.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	98.496, 67.503, 69.638
Angle α, β, γ (deg.)	90.000, 134.920, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	CRISPR-associated protein, TM1810 family / Csm2 Mass: 17795.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 35984 / RP62A / Gene: SERP2460 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HK90
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.3 Å³/Da / Density % sol: 46.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 180 mM Li2SO4, 90 mM HEPES-Na (pH 7.5), 22.5% (w/v) PEG3350, 10 mM sarcosine

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Data collection

Diffraction

Mean temperature: 95 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-17A / Wavelength: 0.97875 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 22, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97875 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. obs: 12646 / % possible obs: 100 % / Redundancy: 6.6 % / B_iso Wilson estimate: 48.86 Å² / R_merge(I) obs: 0.08 / R_pim(I) all: 0.033 / R_rim(I) all: 0.087 / Χ²: 1.056 / Net I/σ(I): 5.5 / Num. measured all: 84040

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.4-2.44	5.6	0.505	606	0.827	0.23	0.556	0.445	99.8
2.44-2.49	6.5	0.443	678	0.927	0.186	0.481	0.492	99.9
2.49-2.53	6.7	0.367	579	0.944	0.151	0.397	0.456	100
2.53-2.59	6.5	0.322	648	0.937	0.136	0.351	0.475	100
2.59-2.64	6.6	0.303	594	0.955	0.127	0.329	0.461	100
2.64-2.7	7	0.254	660	0.969	0.103	0.274	0.479	100
2.7-2.77	6.8	0.218	607	0.969	0.09	0.236	0.506	100
2.77-2.85	6.8	0.194	625	0.977	0.08	0.21	0.52	100
2.85-2.93	6.5	0.172	651	0.98	0.073	0.187	0.521	100
2.93-3.02	6.9	0.148	650	0.98	0.06	0.16	0.683	100
3.02-3.13	6.7	0.134	624	0.988	0.056	0.145	0.619	100
3.13-3.26	6.7	0.119	593	0.991	0.05	0.129	0.608	100
3.26-3.41	6.9	0.097	641	0.996	0.039	0.105	0.689	100
3.41-3.58	6.6	0.085	644	0.994	0.035	0.092	1.371	100
3.58-3.81	6.7	0.066	621	0.997	0.027	0.071	0.922	100
3.81-4.1	6.6	0.056	647	0.998	0.024	0.061	0.91	100
4.1-4.52	7	0.06	629	0.995	0.024	0.065	1.936	100
4.52-5.17	6.7	0.057	637	0.997	0.024	0.062	1.379	100
5.17-6.51	6.7	0.072	652	0.996	0.03	0.078	2.196	100
6.51-50	6.4	0.057	660	0.997	0.024	0.062	5.237	100

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	1.11.1_2575	refinement
PDB_EXTRACT	3.24	data extraction
HKL-2000		data reduction
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.405→49.308 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.36

	R_factor	Num. reflection	% reflection
R_free	0.233	615	4.86 %
R_work	0.212	-	-
obs	0.213	12643	99.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 147.07 Å² / B_iso mean: 61.7128 Å² / B_iso min: 33.44 Å²

Refinement step

Cycle: final / Resolution: 2.405→49.308 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1938	0	0	2	1940
B_iso mean	-	-	-	55.88	-
Num. residues	-	-	-	-	228

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	1976
X-RAY DIFFRACTION	f_angle_d	0.376	2646
X-RAY DIFFRACTION	f_chiral_restr	0.032	286
X-RAY DIFFRACTION	f_plane_restr	0.002	328
X-RAY DIFFRACTION	f_dihedral_angle_d	1.998	1194

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 4

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4051-2.6471	0.2597	148	0.2478	2945	3093	99
2.6471-3.0301	0.2585	150	0.2256	3043	3193	100
3.0301-3.8174	0.2407	162	0.2154	2969	3131	100
3.8174-49.3188	0.2161	155	0.2003	3071	3226	100

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	8.5184	0.7662	2.5268	2.0756	-2.0148	9.0725	-0.6808	0.1844	-0.5093	-0.2931	0.389	-1.1392	-0.073	1.1264	0.1674	0.3982	-0.093	0.0087	0.865	0.06	0.6507	47.335	28.017	7.612
2	5.0197	-1.392	-1.1165	7.398	1.8792	7.8384	0.0481	-0.0879	0.1924	0.336	0.2563	0.5154	0.3344	-0.7856	-0.2648	0.4119	0.0479	0.001	0.5122	0.0801	0.5472	31.828	31.629	2.222
3	7.4373	0.4249	-1.7898	6.5015	-0.2839	2.0517	0.3412	0.9624	-1.7429	-0.7843	-0.0328	-0.1517	2.2262	0.3016	-0.4199	0.929	0.0367	-0.1901	0.8549	-0.2641	0.9954	32.799	17.332	-15.276
4	9.0715	-0.9421	-0.6325	2.0873	0.9205	9.7892	0.2964	1.0269	-0.3842	-0.9911	0.3259	0.8899	0.4527	-0.6974	-0.6233	0.5706	-0.0224	-0.0809	0.5076	0.0911	0.5388	31.691	31.455	-12.689
5	6.2547	-1.9446	2.1485	2.7799	-1.4843	3.6007	-0.2191	-0.0125	-0.1266	0.2275	0.3173	0.214	-0.2682	-0.2679	-0.0861	0.4143	-0.0042	0.0103	0.4054	0.0652	0.4431	37.262	37.573	-2.448
6	6.1241	0.7412	2.5077	3.2034	0.3519	8.5145	0.1657	0.4108	-0.7993	-0.2299	0.1318	0.1735	1.0118	0.4654	-0.2777	0.3685	0.0206	-0.0509	0.2941	-0.0039	0.5085	39.75	24.497	-3.991
7	4.6794	0.3235	-0.0491	4.3097	-0.2518	3.103	0.0195	-0.0197	0.259	0.045	0.1163	0.0286	-0.2662	-0.1491	-0.0607	0.4537	-0.0349	-0.0081	0.5639	-0.0425	0.4098	20.138	13.687	12.834
8	2.7572	-0.4582	4.5827	5.6201	0.7953	8.0559	0.1676	-0.0305	-1.7318	0.2852	0.203	-0.7028	1.1794	1.1191	-0.2464	0.9106	0.2189	0.1065	0.7145	-0.06	0.8981	39.776	0.767	8.01
9	9.0893	-0.9252	-0.3081	2.1673	0.8044	9.845	-0.627	0.525	-0.2191	-0.9943	0.381	-1.2863	0.5626	1.0889	0.3048	0.5332	-0.1154	0.0988	0.5372	0.0477	0.5322	36.946	15.455	7.526
10	3.2088	0.911	-1.8478	4.1158	-4.2468	7.508	0.0455	0.1701	-0.0464	0.1434	0.1133	0.3347	0.1721	0.0467	-0.0781	0.3872	-0.0778	-0.0054	0.3539	0.0169	0.39	25.92	20.92	12.243
11	8.6369	-1.5668	-1.5868	8.5986	2.7683	7.0402	-0.229	-0.995	-1.0804	-0.2286	0.1716	-0.6674	1.0402	1.3707	0.0448	0.5502	0.142	0.0761	0.6698	0.0153	0.5251	37.135	7.596	16.928
12	1.2527	0.3119	-0.9651	3.9371	0.3723	5.9137	-0.1398	0.7302	-1.0128	-0.3068	0.0117	-0.1855	0.6228	-0.4507	0.1727	0.488	-0.0698	0.02	0.3621	-0.0249	0.3605	19.831	8.821	13.463

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:12 )	A	1 - 12
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 13:45 )	A	13 - 45
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 46:62 )	A	46 - 62
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 63:72 )	A	63 - 72
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 73:93 )	A	73 - 93
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 94:125 )	A	94 - 125
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 1:44 )	B	1 - 44
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 45:62 )	B	45 - 62
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 63:73 )	B	63 - 73
10	X-RAY DIFFRACTION	10	( CHAIN B AND ( RESID 74:90 OR RESID 91:91 ) )	B	74 - 90
11	X-RAY DIFFRACTION	10	( CHAIN B AND ( RESID 74:90 OR RESID 91:91 ) )	B	91
12	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 92:109 )	B	92 - 109
13	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 110:125 )	B	110 - 125

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