PDB-5h1o: CRISPR-associated protein

ID or keywords:

Entry

Database: PDB / ID: 5h1o

Title

CRISPR-associated protein

Components

CRISPR-associated endoribonuclease Cas2

Keywords

HYDROLASE / CRISPR-associated protein / Endonuclease

Function / homology

Function and homology information

maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function

Biological species

Xanthomonas albilineans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Ka, D. / Jeong, U. / Bae, E.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Struct Dyn / Year: 2017
Title: Structural and dynamic insights into the role of conformational switching in the nuclease activity of the Xanthomonas albilineans Cas2 in CRISPR-mediated adaptive immunity
Authors: Ka, D. / Hong, S. / Jeong, U. / Jeong, M. / Suh, N. / Suh, J.Y. / Bae, E.

History

Deposition	Oct 11, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5h1o.cif.gz	88 KB	Display	PDBx/mmCIF format
PDB format	pdb5h1o.ent.gz	66.8 KB	Display	PDB format
PDBx/mmJSON format	5h1o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5h1o_validation.pdf.gz	444.9 KB	Display	wwPDB validaton report
Full document	5h1o_full_validation.pdf.gz	446.7 KB	Display
Data in XML	5h1o_validation.xml.gz	10.6 KB	Display
Data in CIF	5h1o_validation.cif.gz	14.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h1/5h1o ftp://data.pdbj.org/pub/pdb/validation_reports/h1/5h1o	HTTPS FTP

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Related structure data

Related structure data	5h1pC 4es2S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2pa0-1 6l50-4 3bya-d 1bc7-d 5h1p-d 4ae5-2 4d5t-2 5gpi-2 5yod-3 1v4p-2 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: CRISPR-associated endoribonuclease Cas2

B: CRISPR-associated endoribonuclease Cas2

hetero molecules

24.1 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)	90.385, 90.385, 50.831
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

#1: Protein	CRISPR-associated endoribonuclease Cas2 Mass: 11945.717 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas albilineans (strain GPE PC73 / CFBP 7063) (bacteria) Strain: GPE PC73 / CFBP 7063 / Gene: cas2, XALc_2892 / Production host: Escherichia coli (E. coli) References: UniProt: D2UG58, Hydrolases; Acting on ester bonds
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.51 Å³/Da / Density % sol: 50.97 %
Crystal grow	Temperature: 293 K / Method: evaporation Details: 50mM Ammonium acetate, 85mM Sodium acetate pH 4.6, 23%(w/v) PEG4000. 10%(v/v) Glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.65→50 Å / Num. obs: 28581 / % possible obs: 99.7 % / Redundancy: 12.1 % / R_merge(I) obs: 0.071 / Net I/σ(I): 12.6
Reflection shell	Resolution: 1.65→1.71 Å / Redundancy: 11.5 % / R_merge(I) obs: 0.809 / Mean I/σ(I) obs: 3.1 / CC_1/2: 0.899 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data collection
HKL-2000		data processing
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ES2

4es2

Resolution: 1.65→29.585 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.05

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2052	1917	7.1 %	1
R_work	0.1656	-	-	-
obs	0.1683	27006	94.18 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→29.585 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1353	0	12	175	1540

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	1388
X-RAY DIFFRACTION	f_angle_d	1.413	1867
X-RAY DIFFRACTION	f_dihedral_angle_d	13.165	519
X-RAY DIFFRACTION	f_chiral_restr	0.072	203
X-RAY DIFFRACTION	f_plane_restr	0.008	241

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6488-1.6901	0.2295	112	0.2261	1532	X-RAY DIFFRACTION	82
1.6901-1.7358	0.2669	126	0.2085	1645	X-RAY DIFFRACTION	86
1.7358-1.7868	0.2243	128	0.2007	1663	X-RAY DIFFRACTION	88
1.7868-1.8445	0.2097	135	0.196	1712	X-RAY DIFFRACTION	90
1.8445-1.9104	0.2591	137	0.1848	1711	X-RAY DIFFRACTION	91
1.9104-1.9869	0.2313	131	0.1778	1821	X-RAY DIFFRACTION	95
1.9869-2.0773	0.2221	142	0.1781	1819	X-RAY DIFFRACTION	97
2.0773-2.1868	0.2377	142	0.1772	1863	X-RAY DIFFRACTION	98
2.1868-2.3237	0.2179	142	0.1735	1862	X-RAY DIFFRACTION	98
2.3237-2.5031	0.2232	141	0.1782	1854	X-RAY DIFFRACTION	98
2.5031-2.7548	0.2038	143	0.1775	1894	X-RAY DIFFRACTION	99
2.7548-3.153	0.2056	148	0.1695	1901	X-RAY DIFFRACTION	99
3.153-3.9709	0.1889	147	0.1493	1918	X-RAY DIFFRACTION	100
3.9709-29.5902	0.1871	143	0.1494	1894	X-RAY DIFFRACTION	96

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	4.018	2.5922	4.193	4.5556	6.2174	3.299	-0.1247	0.0552	0.5572	0.033	-0.0723	0.3619	-0.1099	0.0071	0.4054	0.2754	-0.013	-0.0617	0.2708	0.0427	0.289	25.2757	49.4958	28.7595
2	7.0592	-1.858	-2.5355	6.697	-7.6078	1.9742	-0.0457	-0.0948	1.9845	1.5996	-0.45	-0.4521	-3.0393	1.1625	0.431	0.7767	-0.3166	-0.3693	0.6203	0.2336	1.1775	37.6556	62.5024	31.1027
3	3.9246	3.1105	2.0873	3.3974	2.1257	9.5642	0.088	0.4975	-0.4503	-0.4509	-0.3506	-1.2146	-0.0771	0.83	0.1506	0.2892	0.031	-0.0101	0.4856	0.1202	0.4353	35.8386	47.4351	26.2793
4	4.5714	-2.4011	3.6345	7.8444	-6.1884	8.9243	0.3585	0.0851	-0.2806	-0.2113	-0.149	-0.0671	0.4834	0.0565	-0.1886	0.2283	0.004	-0.0388	0.2842	0.0048	0.2467	27.0923	44.0619	27.1797
5	7.345	-1.4644	0.4835	5.8183	-2.0332	2.0433	-0.11	-0.2584	0.2622	0.3704	0.0337	-0.4252	-0.2189	0.0227	0.0894	0.2423	-0.0012	-0.0589	0.2628	0.0086	0.2018	28.399	50.22	35.2963
6	5.5224	5.6027	-6.0806	5.1015	-6.1329	6.9716	0.0065	0.4735	-0.0205	0.1611	-0.03	0.2077	-0.1533	-0.508	-0.0259	0.2758	-0.0019	-0.0174	0.3511	-0.0283	0.2721	13.4682	44.3509	19.4489
7	6.6623	6.1823	-4.721	5.7393	-4.41	3.4566	0.2901	0.9078	-1.0196	-0.5715	-0.0161	-0.8603	0.5977	0.1411	0.0504	0.3998	0.1008	0.0995	0.4286	0.0222	0.4388	23.8623	54.6351	12.261
8	4.2779	1.3558	-6.5885	7.4693	-4.0358	8.9565	0.1149	-0.1656	0.5633	-0.026	-0.3066	-0.3582	-0.2738	0.3801	0.1531	0.1995	0.0123	-0.0403	0.2095	0.061	0.2435	17.0494	57.3422	22.8733
9	4.1982	-5.0533	-3.476	6.168	4.2461	3.0934	-0.0894	0.8528	0.8937	-0.0062	-0.6653	-3.3075	-1.3171	1.9331	0.2791	0.7239	-0.1458	0.0747	0.6945	0.2575	1.2611	27.9842	69.5533	18.643
10	2.6284	3.0902	-3.4412	3.6747	-4.0777	4.5227	-0.1866	0.5082	1.2913	-0.3165	0.1755	-0.466	-0.9173	0.3012	0.1033	0.409	-0.0589	-0.0224	0.3209	0.0286	0.4288	19.0167	69.699	21.6426
11	2.3127	0.661	2.0735	2.1517	-1.5783	6.4989	0.1002	-0.3673	0.5557	0.564	-0.0525	0.0758	-0.896	-0.2624	0.0053	0.3329	-0.003	-0.0286	0.2218	-0.0201	0.3233	12.5179	65.3747	28.7464
12	7.4926	-1.6535	2.8403	2.9872	-0.1154	3.5811	0.0059	-0.0242	0.0447	0.0859	-0.0839	0.0127	-0.0906	0.0413	0.0688	0.2616	-0.0009	-0.0094	0.22	0.0289	0.2325	11.667	59.4094	24.6807
13	2.9428	-1.1714	0.5611	3.4653	0.2917	1.0599	0.1914	0.4321	0.3854	-0.4047	-0.2448	-0.3819	-0.122	0.1085	0.0477	0.2243	0.0537	0.0399	0.2691	0.0711	0.211	16.6286	59.2687	16.6509
14	3.8008	1.3897	5.4898	3.7992	0.6935	8.1617	0.1101	-0.5715	0.2286	0.6168	-0.0798	0.0124	0.007	-0.3767	0.0388	0.323	0.0277	0.0023	0.3146	0.0163	0.2072	17.122	51.2598	36.2199

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 9 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 17 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 18 through 32 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 33 through 51 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 52 through 72 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 73 through 80 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 81 through 86 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 9 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 10 through 18 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 19 through 26 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 27 through 33 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 34 through 50 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 51 through 73 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 74 through 85 )

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