PDB-6en0: Structure of the Tn1549 transposon Integrase (aa 82-397) in compl...

ID or keywords:

Entry

Database: PDB / ID: 6en0

Title

Structure of the Tn1549 transposon Integrase (aa 82-397) in complex with circular intermediate DNA (CI5-DNA)

Components

(DNA (44-MER)) x 2
Int protein

Keywords

RECOMBINATION /

transposase protein - DNA complex / tyrosine recombinase / Y-transposase / Tn916-like conjugative transposon / antibiotic resistance transfer

Function / homology

Function and homology information

integrase activity / viral genome integration into host DNA / establishment of integrated proviral latency / DNA recombination / symbiont entry into host cell /

Biological species

Enterococcus faecalis (bacteria)

Clostridioides difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Rubio-Cosials, A. / Barabas, O.

Citation

Journal: Cell / Year: 2018
Title: Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.
Authors: Rubio-Cosials, A. / Schulz, E.C. / Lambertsen, L. / Smyshlyaev, G. / Rojas-Cordova, C. / Forslund, K. / Karaca, E. / Bebel, A. / Bork, P. / Barabas, O.

History

Deposition	Oct 4, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 4, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	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	6en0.cif.gz	324.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6en0.ent.gz	258.9 KB	Display	PDB format
PDBx/mmJSON format	6en0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/en/6en0 ftp://data.pdbj.org/pub/pdb/validation_reports/en/6en0	HTTPS FTP

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Related structure data

Related structure data	6emyC 6emzSC 6en1C 6en2C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5wg6-1 2ant-d 5vn5-d 1br8-d 7bwg-d 4arv-d 6rrq-d 2ox6-d 6en2-d 1nwg-d 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #84 - Dec 2006 Transposase similarity (10) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #135 - Mar 2011 Integrase similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #73 - Jan 2006 Topoisomerase similarity (2) #87 - Mar 2007 Zinc Fingers similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #160 - Apr 2013 Actinomycin similarity (2) #39 - Mar 2003 lac Repressor similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #131 - Nov 2010 Inteins similarity (1) #125 - May 2010 Parvoviruses similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#84 - Dec 2006
Transposase
similarity (10)
#253 - Jan 2021
Expressome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#122 - Feb 2010
Enhanceosome
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#135 - Mar 2011
Integrase
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (2)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (2)
#39 - Mar 2003
lac Repressor
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Int protein

C: DNA (44-MER)

E: DNA (44-MER)

B: Int protein

99.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software
Evidence: gel filtration, SAXS

Unit cell

Length a, b, c (Å)	77.660, 124.320, 77.400
Angle α, β, γ (deg.)	90.00, 117.69, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Int protein / Integrase Mass: 36286.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: int / Plasmid: pETM28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q7BP35
#2: DNA chain	DNA (44-MER) Mass: 13607.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Circular intermediate DNA / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain	DNA (44-MER) Mass: 13469.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Circular intermediate DNA / Source: (synth.) Clostridioides difficile (bacteria)
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.32 Å³/Da / Density % sol: 62.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na Acetate pH4.6, 30% PEG300

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.8→46.044 Å / Num. obs: 31128 / % possible obs: 96.6 % / Redundancy: 2.85 % / CC_1/2: 0.995 / R_rim(I) all: 0.125 / R_sym value: 0.102 / Net I/σ(I): 10.67
Reflection shell	Resolution: 2.8→2.87 Å / Redundancy: 2.87 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 2363 / CC_1/2: 0.622 / R_rim(I) all: 1.739 / R_sym value: 1.415 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PHASER		phasing
XDS		data scaling
Coot		model building
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6EMZ

6emz

Resolution: 2.8→46.044 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.15

	R_factor	Num. reflection	% reflection
R_free	0.2543	1625	5.22 %
R_work	0.2268	-	-
obs	0.2283	31128	96.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→46.044 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4502	1355	0	60	5917

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6112
X-RAY DIFFRACTION	f_angle_d	0.579	8584
X-RAY DIFFRACTION	f_dihedral_angle_d	20.97	2219
X-RAY DIFFRACTION	f_chiral_restr	0.023	971
X-RAY DIFFRACTION	f_plane_restr	0.003	888

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 (%)
2.8009-2.8913	0.3977	135	0.4081	2764	X-RAY DIFFRACTION	94
2.8913-2.9945	0.4063	155	0.3744	2709	X-RAY DIFFRACTION	93
2.9945-3.1143	0.3159	138	0.3401	2707	X-RAY DIFFRACTION	94
3.1143-3.256	0.335	140	0.3017	2673	X-RAY DIFFRACTION	92
3.256-3.4275	0.3416	146	0.2736	2640	X-RAY DIFFRACTION	91
3.4275-3.642	0.294	129	0.2644	2641	X-RAY DIFFRACTION	91
3.642-3.9227	0.354	137	0.2667	2634	X-RAY DIFFRACTION	90
3.9227-4.3167	0.2762	143	0.2309	2706	X-RAY DIFFRACTION	92
4.3167-4.9396	0.2095	131	0.1904	2652	X-RAY DIFFRACTION	92
4.9396-6.2167	0.241	159	0.1838	2703	X-RAY DIFFRACTION	92
6.2167-33.1752	0.174	157	0.1725	2692	X-RAY DIFFRACTION	90

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	3.9201	1.101	2.3272	2.5407	-1.1107	2.6705	0.0442	-0.163	0.0466	0.7427	-0.14	0.1614	0.5349	-0.0251	0.3793	0.8701	-0.1069	0.186	0.6979	-0.1114	0.6654	41.1572	-23.9027	43.1722
2	1.3574	-0.1363	0.4421	2.5383	-2.0171	2.7854	-0.271	0.0085	0.1916	0.1129	-0.0535	0.2735	-0.4466	0.61	0.7039	0.5502	-0.0818	-0.0251	0.4562	-0.1226	0.7675	46.8258	-15.4452	35.011
3	3.379	0.4245	2.5168	1.707	-0.6727	2.5547	-0.2786	-0.3319	0.3569	0.1649	0.2267	0.5961	-1.0084	0.0903	-0.2995	0.6667	0.0686	0.0787	0.4425	-0.14	0.8069	36.8607	-10.9642	33.2367
4	3.2612	-0.1071	1.8399	2.2089	-0.6269	0.7478	-0.678	0.223	-0.3697	-0.4846	-0.0057	-0.3307	0.4056	-0.393	0.2167	0.9176	0.0193	0.2007	0.4282	-0.0198	0.9142	25.0639	-30.4691	5.3588
5	6.3021	0.8117	2.0132	2.8118	2.2993	2.2932	-0.4543	0.2302	0.2051	0.5794	-0.2025	0.6002	-0.3852	-0.0795	0.2892	0.6887	-0.0147	0.21	0.3401	0.1392	0.8364	26.2977	-35.0462	19.5159
6	2.3145	-0.5834	0.757	1.916	-2.3114	5.2792	0.0009	0.1234	0.0627	-1.1094	-0.3135	0.2187	0.8874	-0.4744	0.2923	1.0859	-0.0584	-0.1193	0.3422	0.0557	0.8625	23.9997	-41.3567	6.6491
7	0.8337	0.4821	-1.593	-0.0959	0.4428	7.1324	-0.7371	-0.5034	-0.5671	-1.2445	0.0548	-0.7269	2.1914	0.0902	0.4762	1.0523	-0.1465	0.1849	0.5488	-0.0354	0.9749	31.5896	-41.9446	13.4574
8	3.6041	0.0588	-1.99	2.0523	-1.3214	4.0881	0.1529	0.2734	1.5498	-0.4104	0.1021	-0.4827	-0.341	-0.0064	-0.0621	0.6516	0.0592	0.0566	0.4844	0.1034	0.9392	32.2093	-21.0226	6.3436
9	1.5399	-1.7143	-1.1825	1.4707	0.5723	1.6647	0.8695	0.2022	0.0264	-3.3549	-0.2166	0.0031	1.3036	-0.04	-0.3926	1.2535	-0.1577	-0.0469	0.7602	-0.2509	1.0677	13.7485	-11.0736	16.7167
10	0.6374	1.6212	-0.8333	4.8602	0.2401	1.9235	0.3208	0.2299	0.3898	-0.5853	-0.6178	0.35	-0.2117	0.4245	0.2887	0.6633	0.2128	0.062	0.6695	0.1664	0.9194	48.0563	-30.5675	10.0648
11	1.6556	-2.4845	-3.4458	1.3201	1.7476	3.0828	-0.4787	0.5832	-0.2744	0.7755	0.5474	1.1745	-0.2256	-0.9029	-0.3691	0.9254	0.019	0.4246	0.8943	-0.0575	1.5436	24.9729	-15.0042	32.1417
12	2.5795	1.5073	-0.4881	3.117	1.7663	0.5597	-0.5806	-0.1788	0.4193	-0.3943	-0.2199	0.356	-0.0029	-0.2292	0.9104	1.0739	0.074	0.2446	0.6582	-0.0211	1.0481	-10.2852	7.0526	45.0225
13	1.9599	2.7196	2.6566	3.2427	2.4923	2.1649	0.6205	-0.2306	0.6065	0.1963	-0.9615	0.819	0.7497	-0.2134	0.2249	1.0742	0.1119	0.3907	0.5726	0.022	1.1098	-9.5552	7.9442	46.5046
14	5.8516	-5.8305	-4.7224	4.4498	3.1653	-0.5075	0.6435	-0.3063	0.8989	-0.4228	-0.1926	-0.5427	-0.5309	0.1081	-0.4429	0.8969	0.0289	0.1578	0.706	-0.1371	1.0158	20.2035	-13.0379	35.3363
15	2.9996	-1.4457	2.0939	2.0813	0.3112	1.3003	0.8398	1.7619	-0.5705	-0.7778	-0.3927	-1.9582	-0.1549	0.2521	-0.5977	0.7208	0.1101	0.2231	0.784	-0.0591	1.6018	48.0601	-30.2041	10.8901
16	4.1804	-0.2336	2.7597	0.5097	-0.5937	1.5318	-0.1358	-0.4502	-0.3239	0.8483	-0.2819	-1.2704	-1.3938	0.0944	-0.6661	0.9647	0.0537	0.2302	0.6135	0.0478	1.1962	18.9441	0.627	55.8546
17	3.7911	-1.3799	1.2982	5.8421	1.8902	3.7532	0.3784	-0.9216	0.1261	0.2138	-0.4379	-1.0992	0.0766	0.1773	-0.1529	0.7632	0.0814	0.1044	0.6796	0.2427	0.8671	11.1331	-2.6835	57.1889
18	1.4689	0.0372	0.7869	0.6808	1.5864	5.8468	0.8308	-0.82	-0.9664	0.6178	-1.3549	-0.6838	2.9138	-0.6198	-0.4834	0.8312	0.1493	-0.0642	0.2355	0.3953	2.0111	5.5614	-13.9514	56.1758
19	3.3238	0.8415	3.2605	1.2148	1.2491	4.5247	-0.0935	-0.4453	-1.3327	-0.7397	0.0058	-1.5448	0.872	0.5556	-0.3267	0.8828	0.1385	0.1318	0.5823	0.1174	1.4141	16.2515	-12.1316	50.4685
20	1.6096	1.5959	1.5814	1.3833	-0.1724	5.1656	0.0223	0.5685	-0.9591	-1.4037	-0.1657	0.0967	1.2226	-0.1757	0.3637	0.9762	-0.0072	0.1341	0.6577	-0.0402	0.9456	-10.6382	-6.1639	29.3161
21	3.4701	2.0597	-0.5753	5.0678	3.5114	4.9151	0.0298	0.3483	0.0136	-1.2465	0.4009	-0.0818	-1.0888	-0.3004	-0.3864	0.8561	0.0519	0.022	0.4412	0.1136	0.4831	-4.6441	10.2382	24.98
22	0.0006	-0.179	1.8001	5.4659	3.4641	3.705	0.3069	0.2163	-0.1875	0.0556	0.1832	-0.3713	0.2879	0.4664	-0.9713	0.699	0.1037	0.1458	0.5087	0.0848	0.7717	6.9835	11.5397	30.8142
23	2.6144	2.8189	0.0411	5.662	1.1341	2.0134	0.8496	0.8129	0.0185	-1.6552	0.2228	-0.9729	-1.4491	-0.5257	-0.0353	1.3185	0.0501	0.3203	0.3075	-0.2964	0.9479	-5.9882	17.9183	24.5018
24	1.1009	-1.0376	-0.6383	4.6216	1.9864	3.2173	0.2889	0.168	-0.0223	-0.3227	-0.2743	0.0699	-0.3723	-0.3515	0.0429	0.66	-0.0705	0.0368	0.3582	-0.0767	0.6245	-7.2495	4.214	31.7828
25	3.5584	-1.8271	-1.2713	5.2775	2.0123	3.108	0.4354	-0.1203	-0.2787	-0.0673	0.1441	0.5875	-0.4859	0.169	-0.6343	0.555	0.0149	0.0806	0.6045	-0.2581	0.9442	8.2723	-12.4923	18.3035

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 81 through 99 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 100 through 144 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 145 through 192 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 193 through 242 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 243 through 275 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 276 through 297 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 298 through 314 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 315 through 356 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 357 through 394 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid -15 through -5 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid -4 through 5 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 6 through 20 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid -13 through -5 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid -4 through 8 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 9 through 18 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 82 through 99 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 100 through 128 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 129 through 144 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 145 through 180 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 181 through 205 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 206 through 242 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 243 through 275 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 276 through 297 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 298 through 356 )
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 357 through 396 )

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