PDB-6njy: Type IV CRISPR associated RNA endonuclease Cas6 - apo form

ID or keywords:

Entry

Database: PDB / ID: 6njy

Title

Type IV CRISPR associated RNA endonuclease Cas6 - apo form

Components

Type IV CRISPR associated Cas6 RNA endonuclease

Keywords

RNA BINDING PROTEIN / CRISPR / Cas / Nuclease / RNA / Cas6 / Csf5

Function / homology

CRISPR-associated protein Cas6, C-terminal / CRISPR-associated endoribonuclease Cas6 / Alpha-Beta Plaits - #1900 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / beta-D-glucopyranose / CRISPR-associated protein Cas6 C-terminal domain-containing protein

Function and homology information

Biological species

Mahella australiensis

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.76 Å

Authors

Jackson, R.N. / Warner, E. / Olsen, K.J.

Citation

Journal: Rna Biol. / Year: 2019
Title: Structural basis of Type IV CRISPR RNA biogenesis by a Cas6 endoribonuclease.
Authors: Taylor, H.N. / Warner, E.E. / Armbrust, M.J. / Crowley, V.M. / Olsen, K.J. / Jackson, R.N.

History

Deposition	Jan 4, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Sep 11, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Mar 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6njy.cif.gz	294.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nj/6njy ftp://data.pdbj.org/pub/pdb/validation_reports/nj/6njy	HTTPS FTP

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Related structure data

Similar structure data	4gki-18 3c20-1 3c20-2 2iyc-d 4gki-13 1e9h-2 3r6s-4 4gkh-18 1tcr-d 1l2w-6 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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 (2) #198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Type IV CRISPR associated Cas6 RNA endonuclease

B: Type IV CRISPR associated Cas6 RNA endonuclease

hetero molecules

59.1 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, Gel Filtration suggests this protein is a monomer in solution.

Unit cell

Length a, b, c (Å)	85.541, 85.541, 142.587
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

#1: Protein

Type IV CRISPR associated Cas6 RNA endonuclease

Mass: 28278.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mahella australiensis (strain DSM 15567 / CIP 107919 / 50-1 BON) (bacteria)
Strain: DSM 15567 / CIP 107919 / 50-1 BON / Gene: Mahau_2538 / Production host:

Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: F3ZXK6

#2: Chemical

ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO₄

#3: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.66 Å³/Da / Density % sol: 53.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Mother Liquor = 0.1 M sodium acetate trihydrate (pH 5.0) and 1.75M ammonium sulfate. 6-8 mg/ml of protein purified in 100 mM HEPES pH 7.5, 150 mM KCl, 5% glycerol, 1mM TCEP, was mixed in ...Details: Mother Liquor = 0.1 M sodium acetate trihydrate (pH 5.0) and 1.75M ammonium sulfate. 6-8 mg/ml of protein purified in 100 mM HEPES pH 7.5, 150 mM KCl, 5% glycerol, 1mM TCEP, was mixed in equal volumes (2 microliters of each) on a sitting drop pedestal with ~500 mL of mother liquor in reservoir. PH range: 4.8-5.2

Crystal

Density Matthews: 2.66 Å³/Da / Density % sol: 53.81 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Mother Liquor = 0.1 M sodium acetate trihydrate (pH 5.0) and 1.75M ammonium sulfate. 6-8 mg/ml of protein purified in 100 mM HEPES pH 7.5, 150 mM KCl, 5% glycerol, 1mM TCEP, was mixed in ...
PH range: 4.8-5.2

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Data collection

Diffraction

Mean temperature: 193 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 1.55, 1.0718

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2018

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.55	1
2	1.0718	1

Reflection

Resolution: 1.76→40.004 Å / Num. obs: 58149 / % possible obs: 99.6 % / Redundancy: 6 % / B_iso Wilson estimate: 33.22 Å² / R_merge(I) obs: 0.053 / R_pim(I) all: 0.023 / R_rim(I) all: 0.058 / Χ²: 1.057 / Net I/σ(I): 18.1

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
1.76-1.82	4.2	0.727	5618	0.736	0.376	0.822	1.011	96.3
1.82-1.9	5.4	0.541	5809	0.884	0.253	0.599	1.088	99.8
1.9-1.98	6	0.331	5805	0.348	0.148	0.364	1.082	99.9
1.98-2.09	6.3	0.213	5843	0.98	0.093	0.233	1.081	100
2.09-2.22	5.8	0.132	5820	0.989	0.06	0.145	1.066	99.9
2.22-2.39	6.6	0.099	5826	0.998	0.042	0.108	1.004	100
2.39-2.63	6.4	0.08	5818	0.995	0.034	0.087	1.016	100
2.63-3.01	6.5	0.065	5846	0.997	0.028	0.071	1.055	99.9
3.01-3.79	6.4	0.052	5842	0.998	0.023	0.057	1.137	99.9
3.79-40	6.6	0.04	5922	0.996	0.017	0.044	1.021	99.9

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
SOLVE		phasing
RESOLVE		model building
PHENIX	1.13_2998	refinement
PDB_EXTRACT	3.24	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 1.76→40.004 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.15

	R_factor	Num. reflection	% reflection
R_free	0.1978	1966	3.45 %
R_work	0.1672	-	-
obs	0.1682	56932	97.55 %

Solvent computation

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

Displacement parameters

B_iso max: 156.69 Å² / B_iso mean: 50.4429 Å² / B_iso min: 1.13 Å²

Refinement step

Cycle: final / Resolution: 1.76→40.004 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3721	0	191	155	4067
B_iso mean	-	-	101.53	49.16	-
Num. residues	-	-	-	-	475

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7603-1.8044	0.3265	125	0.2899	3511	3636	87
1.8044-1.8531	0.2804	133	0.2422	3759	3892	94
1.8531-1.9077	0.2352	135	0.2232	3789	3924	95
1.9077-1.9692	0.2418	142	0.2002	3895	4037	97
1.9692-2.0396	0.2345	143	0.1871	3962	4105	98
2.0396-2.1213	0.2108	140	0.1812	3944	4084	99
2.1213-2.2178	0.203	140	0.1689	3989	4129	99
2.2178-2.3347	0.2086	143	0.1677	3956	4099	99
2.3347-2.481	0.1877	151	0.1673	4000	4151	100
2.481-2.6725	0.2005	144	0.1764	4019	4163	100
2.6725-2.9414	0.2035	146	0.1858	4010	4156	100
2.9414-3.3668	0.1958	138	0.1795	4022	4160	100
3.3668-4.2411	0.1786	144	0.1483	4038	4182	100
4.2411-40.0138	0.1878	142	0.1468	4072	4214	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	2.8318	-0.5664	-0.6597	1.4425	-0.3688	2.2243	0.049	-0.1095	0.0402	0.1415	-0.0264	0.0197	-0.1507	0.2124	0.0001	0.278	-0.0082	0.0456	0.2085	0.0025	0.2304	-18.7771	21.8019	118.789
2	1.183	1.3269	0.5267	1.4077	-0.0127	2.048	0.3375	0.2588	-0.3989	-0.1906	-0.1479	-0.9753	0.7509	0.4396	0.0003	0.4992	0.0511	-0.0594	0.4048	-0.032	0.5763	-17.838	5.4195	92.3308
3	0.4051	0.1336	-0.0387	0.4847	0.636	0.6793	-0.0692	0.5297	0.2403	-0.4707	-0.0692	0.108	-0.4141	-0.4459	0.0002	0.4553	0.1101	-0.0529	0.4278	0.0791	0.4246	-34.0505	35.5629	77.937
4	2.083	-0.2552	-1.3353	2.7362	-0.302	1.7272	0.1669	-0.0964	0.0102	-0.1361	0.0623	-0.0813	-0.3369	0.0814	0.0001	0.3691	-0.0029	0.0228	0.3176	0.0398	0.4114	-24.8912	37.2848	84.3662
5	0.4182	0.2148	-0.3748	0.9961	-0.0513	2.1646	0.0446	-0.0142	-0.0051	0.1433	0.0071	0.5565	-0.1293	-0.3674	0.0001	0.2435	0.0135	-0.0301	0.3497	0.002	0.461	-34.1994	26.1679	85.8926
6	1.3957	-1.5318	-0.767	1.7705	0.0351	2.4951	-0.1179	0.0774	0.4118	-0.0957	0.1497	-0.1739	-0.2597	0.2924	-0	0.283	-0.0203	-0.0217	0.3389	0.0234	0.2602	-15.4269	23.3377	70.9962
7	1.439	-0.3845	-0.2566	0.5294	-0.0371	1.4418	-0.029	-0.0899	-0.0007	0.2467	0.1359	-0.3072	0.1489	0.4387	0.0004	0.2708	-0.0053	0.0062	0.333	0.0072	0.2367	-12.9812	15.5246	83.3356
8	1.3793	0.0164	-0.6101	0.8485	-0.4081	1.9966	0.1768	0.3697	0.2408	-0.9498	0.03	-0.2682	-0.6139	0.3256	0.0169	0.5169	-0.0139	-0.0807	0.4728	0.1011	0.3307	-20.7442	31.0207	65.3601
9	0.9209	-0.623	-0.3047	1.7365	0.6606	2.9172	-0.0201	0.0806	-0.0967	0.0633	0.0429	0.2318	0.1056	0.0595	-0	0.2176	-0.0209	0.0024	0.2911	0.0355	0.2673	-20.3934	17.3511	76.9986
10	1.31	0.4751	-0.0983	0.7622	-0.0127	1.3154	-0.009	0.0703	-0.9368	0.0609	0.1244	0.1176	0.2804	0.3828	0.0035	0.3543	0.0111	0.0401	0.3833	-0.0405	0.4401	-4.0807	18.2759	100.9602
11	0.0206	-0.0737	0.1548	0.3988	-0.2593	0.4406	0.4263	-0.3539	0.01	0.343	-0.0644	0.2823	-0.8063	0.0013	-0	0.401	0.0679	0.1581	0.3044	0.0282	0.4374	-33.1424	36.0985	115.498
12	0.6676	-0.591	-0.1321	0.8622	-0.4828	0.4206	0.0601	0.1624	-0.3684	-0.3133	-0.0487	0.0482	0.0011	-0.6243	0.0003	0.3918	0.0107	0.0474	0.393	0.0814	0.4633	-37.9161	26.3455	105.0568
13	1.1919	-0.3727	0.8009	1.6474	-0.4235	2.219	-0.0223	0.1442	-0.0918	0.0201	0.1655	0.1776	-0.0748	-0.3632	0	0.3481	0.0683	0.0854	0.3105	0.0385	0.3407	-32.559	32.6696	108.7946
14	0.648	-0.4664	-0.717	0.0579	-1.0844	1.5209	0.0495	-0.1191	0.6926	0.058	0.0932	-0.2448	-0.4416	0.1237	-0.0001	0.428	-0.0265	0.0187	0.3651	-0.0788	0.4522	-15.8027	35.3901	109.5447
15	2.3068	-1.9377	-0.6102	1.7532	-1.0405	3.1289	0.0944	-0.0308	-0.1085	-0.0412	-0.0772	0.5862	0.1519	-0.1528	-0.0005	0.305	0.0136	0.0523	0.2386	0.0105	0.243	-22.8816	16.6529	122.5481
16	0.6459	-0.1474	-0.8903	1.147	-0.5966	2.0317	0.0922	0.1331	-0.2586	-0.088	-0.0386	0.0632	0.3651	0.2937	0.0002	0.2744	0.0202	0.0326	0.266	0.0101	0.245	-14.7064	14.2987	109.9045

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 163 through 229 )	B	163 - 229
2	X-RAY DIFFRACTION	2	chain 'A' and (resid -8 through 10 )	A	-8 - 10
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 11 through 22 )	A	11 - 22
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 23 through 60 )	A	23 - 60
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 61 through 105 )	A	61 - 105
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 106 through 128 )	A	106 - 128
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 129 through 162 )	A	129 - 162
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 163 through 176 )	A	163 - 176
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 177 through 229 )	A	177 - 229
10	X-RAY DIFFRACTION	10	chain 'B' and (resid -7 through 10 )	B	-7 - 10
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 11 through 22 )	B	11 - 22
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 23 through 45 )	B	23 - 45
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 46 through 82 )	B	46 - 82
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 83 through 105 )	B	83 - 105
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 106 through 128 )	B	106 - 128
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 129 through 162 )	B	129 - 162

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