PDB-4xtk: Structure of TM1797, a CAS1 protein from Thermotoga maritima

ID or keywords:

Entry

Database: PDB / ID: 4xtk

Title

Structure of TM1797, a CAS1 protein from Thermotoga maritima

Components

CRISPR-associated endonuclease Cas1

Keywords

HYDROLASE / CAS1 / DNASE / PROKARYOTIC IMMUNE SYSTEM / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG

Function / homology

Function and homology information

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

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Petit, P. / Beloglazova, N. / Skarina, T. / Chang, C. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: Crystal structure and nuclease activity of tm1797, a cas1 protein from thermotoga maritima
Authors: Beloglazova, N. / Skarina, T. / Petit, P. / Flick, R. / Brown, G. / Savchenko, A. / Yakunin, A.F.

History

Deposition	Jan 23, 2015	Deposition site: RCSB / Processing site: RCSB
Supersession	Feb 11, 2015	ID: 3LFX
Revision 1.0	Feb 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4xtk.cif.gz	1004.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4xtk.ent.gz	840.7 KB	Display	PDB format
PDBx/mmJSON format	4xtk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4xtk_validation.pdf.gz	509.5 KB	Display	wwPDB validaton report
Full document	4xtk_full_validation.pdf.gz	549 KB	Display
Data in XML	4xtk_validation.xml.gz	85.3 KB	Display
Data in CIF	4xtk_validation.cif.gz	115.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xt/4xtk ftp://data.pdbj.org/pub/pdb/validation_reports/xt/4xtk	HTTPS FTP

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Related structure data

Related structure data	2yzsS 3god S: Starting model for refinement
Similar structure data	3x16-d 3wxo-d 6mvr-d 4yzs-d 4bhm-d 1fgm-d 3d7t-d 5k4t-1 5k9i-d 4mi4-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
Other databases	TargetTrack: MCSG-APC4937

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#181 - Jan 2015 Cascade and CRISPR similarity (5)

Deposited unit

A: CRISPR-associated endonuclease Cas1

B: CRISPR-associated endonuclease Cas1

C: CRISPR-associated endonuclease Cas1

D: CRISPR-associated endonuclease Cas1

E: CRISPR-associated endonuclease Cas1

F: CRISPR-associated endonuclease Cas1

G: CRISPR-associated endonuclease Cas1

H: CRISPR-associated endonuclease Cas1

309 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CRISPR-associated endonuclease Cas1

E: CRISPR-associated endonuclease Cas1

defined by author&software
77.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: CRISPR-associated endonuclease Cas1

G: CRISPR-associated endonuclease Cas1

defined by author&software
77.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: CRISPR-associated endonuclease Cas1

F: CRISPR-associated endonuclease Cas1

defined by author&software
77.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: CRISPR-associated endonuclease Cas1

H: CRISPR-associated endonuclease Cas1

defined by author&software
77.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.277, 94.555, 106.390
Angle α, β, γ (deg.)	93.03, 115.06, 102.97
Int Tables number	1
Space group name H-M	P1

#1: Protein	CRISPR-associated endonuclease Cas1 Mass: 38659.414 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: cas1, TM_1797, ThemaDRAFT_1327 / Plasmid: P15-TVL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q9X2B7, Hydrolases; Acting on ester bonds
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

CRISPR-associated endonuclease Cas1

Mass: 38659.414 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: cas1, TM_1797, ThemaDRAFT_1327 / Plasmid: P15-TVL / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9X2B7, Hydrolases; Acting on ester bonds

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.67 Å³/Da / Density % sol: 54 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 20% W/V PEG3350, 0.2M MG NITRATE, 0.3M NACL AND 10MM NH4ACETATE PH 4.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2009
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.7→19.9 Å / Num. obs: 83703 / % possible obs: 97.4 % / Redundancy: 3.9 % / R_merge(I) obs: 0.08 / R_sym value: 0.07 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 3.2 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1702)	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2YZS

2yzs

Resolution: 2.7→19.852 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 24.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2302	4200	5.02 %
R_work	0.1835	-	-
obs	0.1859	83692	97.6 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.7→19.852 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19860	0	0	133	19993

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	20287
X-RAY DIFFRACTION	f_angle_d	1.103	27342
X-RAY DIFFRACTION	f_dihedral_angle_d	14.397	7514
X-RAY DIFFRACTION	f_chiral_restr	0.042	3053
X-RAY DIFFRACTION	f_plane_restr	0.005	3504

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 (%)
2.7-2.7306	0.2761	138	0.2308	2641	X-RAY DIFFRACTION	97
2.7306-2.7626	0.2789	132	0.2402	2670	X-RAY DIFFRACTION	98
2.7626-2.7962	0.2898	145	0.2289	2661	X-RAY DIFFRACTION	97
2.7962-2.8315	0.2885	161	0.223	2588	X-RAY DIFFRACTION	98
2.8315-2.8687	0.2276	127	0.2164	2691	X-RAY DIFFRACTION	98
2.8687-2.9079	0.3069	132	0.2261	2611	X-RAY DIFFRACTION	98
2.9079-2.9493	0.2687	131	0.215	2692	X-RAY DIFFRACTION	98
2.9493-2.9932	0.3093	135	0.2256	2659	X-RAY DIFFRACTION	98
2.9932-3.0398	0.2644	135	0.2143	2664	X-RAY DIFFRACTION	98
3.0398-3.0894	0.2865	146	0.2037	2605	X-RAY DIFFRACTION	98
3.0894-3.1425	0.2405	136	0.2193	2691	X-RAY DIFFRACTION	98
3.1425-3.1994	0.284	119	0.2167	2648	X-RAY DIFFRACTION	98
3.1994-3.2607	0.2907	152	0.2137	2685	X-RAY DIFFRACTION	98
3.2607-3.3269	0.2447	142	0.2095	2662	X-RAY DIFFRACTION	98
3.3269-3.3989	0.2603	148	0.2064	2640	X-RAY DIFFRACTION	98
3.3989-3.4776	0.2385	165	0.1993	2629	X-RAY DIFFRACTION	98
3.4776-3.5641	0.2675	139	0.1898	2675	X-RAY DIFFRACTION	98
3.5641-3.6599	0.2266	160	0.1828	2634	X-RAY DIFFRACTION	98
3.6599-3.7668	0.2307	149	0.1805	2640	X-RAY DIFFRACTION	98
3.7668-3.8876	0.2235	136	0.1727	2622	X-RAY DIFFRACTION	98
3.8876-4.0254	0.2137	156	0.1699	2660	X-RAY DIFFRACTION	98
4.0254-4.1851	0.2163	149	0.1696	2647	X-RAY DIFFRACTION	98
4.1851-4.3737	0.2028	129	0.1528	2633	X-RAY DIFFRACTION	98
4.3737-4.6015	0.1762	143	0.1523	2680	X-RAY DIFFRACTION	98
4.6015-4.8858	0.1903	152	0.1593	2635	X-RAY DIFFRACTION	98
4.8858-5.2566	0.2298	125	0.1769	2657	X-RAY DIFFRACTION	98
5.2566-5.7737	0.2296	134	0.1835	2647	X-RAY DIFFRACTION	97
5.7737-6.5824	0.2618	127	0.2235	2660	X-RAY DIFFRACTION	97
6.5824-8.1949	0.2293	141	0.1805	2630	X-RAY DIFFRACTION	97
8.1949-19.8526	0.1697	116	0.1404	2635	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	4.7206	0.8408	-0.2022	5.7264	1.577	5.0235	0.0514	-0.6902	1.047	0.4476	0.0474	0.3345	-1.6362	-0.3813	-0.0683	0.9651	0.0636	0.1122	0.3905	-0.0839	0.6176	-16.1306	1.859	6.4986
2	4.2893	1.5737	0.6844	4.0482	1.8576	4.7397	0.2394	-0.6846	0.5677	0.6331	-0.1236	-0.6585	-0.6416	0.8227	-0.027	0.6071	-0.1707	-0.0958	0.5303	-0.0277	0.635	7.2884	-0.5424	0.2026
3	7.0106	-0.6001	1.749	5.5801	-1.1452	1.4786	-0.1191	-0.1705	-1.0015	-0.2129	-0.0525	-0.9988	1.3131	0.8032	0.1825	0.8708	0.3936	0.0576	0.9055	-0.0027	0.6863	51.0311	-63.0331	25.0243
4	2.5903	-0.1901	0.3884	2.8985	-2.2388	5.4989	-0.0109	-0.6644	-0.3926	0.1657	0.0092	-0.2075	1.0916	0.5797	-0.0802	0.6254	0.1796	-0.008	0.5963	-0.0103	0.4278	31.9956	-57.9343	39.3695
5	3.4091	1.7387	-1.1254	5.9096	1.9923	3.3715	0.3046	0.5315	-1.7537	-0.1787	-0.0579	0.4458	0.9175	-0.2854	-0.1871	0.6712	0.0614	-0.3313	0.4821	-0.1419	1.162	-3.9864	-66.4829	0.3882
6	3.8281	-0.3625	-0.5763	3.2781	1.7243	6.1747	0.3469	1.2645	-0.5795	-0.9916	-0.2599	-0.1097	0.2445	0.2395	-0.1642	0.6363	0.2047	-0.0879	0.7253	-0.1581	0.4786	14.5096	-54.7098	-11.3503
7	3.0535	-1.1548	-0.6181	5.7865	-3.1986	4.7418	-0.1879	0.5388	1.6023	-0.1924	0.0817	-0.3506	-1.35	0.2611	0.0675	0.9766	-0.1803	0.0025	0.5355	0.128	0.8898	-0.5636	14.4829	-50.5852
8	5.0732	-0.3124	1.8176	3.0069	-1.061	4.1795	-0.4598	0.4585	0.841	-0.4419	0.1582	0.2976	-0.5691	-0.5498	0.2891	0.5353	-0.0179	-0.061	0.463	0.0525	0.49	-20.6903	0.3962	-46.5617
9	4.4454	0.9551	-0.7117	8.0116	1.1785	7.3968	-0.0037	-0.9275	-0.3987	1.0325	0.0008	0.1166	0.0228	-0.3859	-0.017	0.4732	0.0447	0.0214	0.4389	0.0569	0.3589	-17.7202	-15.8822	10.264
10	5.4233	0.7399	2.0115	1.836	0.3519	3.3918	-0.033	0.127	-0.4536	0.0032	0.1391	-0.0046	0.3263	-0.4412	-0.0993	0.3639	-0.0357	0.0783	0.3839	0.0464	0.2904	-24.2281	-25.5709	-20.2363
11	7.9308	0.3975	-1.5093	4.3942	0.5273	7.4307	0.3366	0.5027	-0.7908	-0.3217	-0.1468	1.054	0.0823	-1.2039	-0.2032	0.4222	0.07	-0.1842	0.479	0.0005	0.7551	-13.806	-51.4345	2.4859
12	2.5322	-0.2193	0.0694	2.0047	0.0519	6.598	0.1119	-0.8332	0.215	0.2603	0.1216	0.2981	-0.1572	-0.6173	-0.2253	0.2617	0.0068	0.0323	0.5794	-0.0018	0.4485	1.1824	-39.414	28.0712
13	8.9108	1.3011	-1.3006	4.7887	-2.4584	4.6455	0.2858	-0.3247	0.178	0.0591	-0.5237	-0.7985	-0.1847	1.9081	0.32	0.4615	0.1282	0.0359	1.2339	-0.0443	0.7038	57.9513	-46.4619	26.3313
14	1.6957	0.4216	-1.6476	1.5167	-0.8115	6.7221	0.0599	0.1776	0.3056	-0.2114	0.1859	-0.1816	-0.29	0.4462	-0.2525	0.3235	-0.0718	0.1066	0.5442	-0.0522	0.5334	40.2075	-33.3665	2.5587
15	7.148	0.3318	-0.7829	3.9891	-2.0783	5.323	-0.3939	1.5454	0.1029	-1.0445	0.2273	-0.8086	-0.1466	0.7301	0.2423	0.8698	-0.2589	0.2856	0.7468	0.0243	0.7666	8.1939	1.1892	-58.697
16	6.7045	-0.344	2.942	1.3926	-0.4708	3.5503	0.0117	0.1289	-0.0767	0.0235	-0.0334	-0.364	0.071	0.5988	0.0285	0.3837	-0.0059	0.1515	0.5078	-0.0042	0.5531	19.5121	-13.3381	-32.439

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resseq 2:77)
2	X-RAY DIFFRACTION	2	(chain A and resseq 78:315)
3	X-RAY DIFFRACTION	3	(chain B and resseq 1:77)
4	X-RAY DIFFRACTION	4	(chain B and resseq 78:315)
5	X-RAY DIFFRACTION	5	(chain C and resseq 2:77)
6	X-RAY DIFFRACTION	6	(chain C and resseq 78:318)
7	X-RAY DIFFRACTION	7	(chain D and resseq 2:77)
8	X-RAY DIFFRACTION	8	(chain D and resseq 78:319)
9	X-RAY DIFFRACTION	9	(chain E and resseq 1:77)
10	X-RAY DIFFRACTION	10	(chain E and resseq 78:315)
11	X-RAY DIFFRACTION	11	(chain F and resseq 1:77)
12	X-RAY DIFFRACTION	12	(chain F and resseq 78:315)
13	X-RAY DIFFRACTION	13	(chain G and resseq 3:77)
14	X-RAY DIFFRACTION	14	(chain G and resseq 78:315)
15	X-RAY DIFFRACTION	15	(chain H and resseq 3:77)
16	X-RAY DIFFRACTION	16	(chain H and resseq 78:315)

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