PDB-5cr4: Crystal structure of the Sleeping Beauty transposase catalytic domain

ID or keywords:

Entry

Database: PDB / ID: 5cr4

Title

Crystal structure of the Sleeping Beauty transposase catalytic domain

Components

Sleeping Beauty transposase, SB100X

Keywords

HYDROLASE /

Transposase / Tc1/mariner family / RNaseH fold

Function / homology

Ribonuclease H-like superfamily/Ribonuclease H /

Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta /

CITRIC ACID

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Voigt, F. / Barabas, O.

Citation

Journal: Nat Commun / Year: 2016
Title: Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering.
Authors: Voigt, F. / Wiedemann, L. / Zuliani, C. / Querques, I. / Sebe, A. / Mates, L. / Izsvak, Z. / Ivics, Z. / Barabas, O.

History

Deposition	Jul 22, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 30, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 13, 2016	Group: Database references
Revision 1.2	Mar 7, 2018	Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3	Jan 10, 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	5cr4.cif.gz	226.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5cr4.ent.gz	182.7 KB	Display	PDB format
PDBx/mmJSON format	5cr4.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/cr/5cr4 ftp://data.pdbj.org/pub/pdb/validation_reports/cr/5cr4	HTTPS FTP

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Related structure data

Related structure data	3hosS S: Starting model for refinement
Similar structure data	5jmd-d 3ktd-1 4o1g-1 3ktd-2 4q8q-1 2nso-1 5byc-d 2jgv-1 3pds-d 1wke-2 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	#84 - Dec 2006 Transposase similarity (1)

Deposited unit

A: Sleeping Beauty transposase, SB100X

B: Sleeping Beauty transposase, SB100X

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	84.240, 113.980, 144.940
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	24
Space group name H-M	I2₁2₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-308- SO4
2	1	A-472- HOH
3	1	A-614- HOH
4	1	B-405- HOH
5	1	B-447- HOH
6	1	B-569- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Sleeping Beauty transposase, SB100X Mass: 26664.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pETM22 / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 5 types, 759 molecules

#2: Chemical	... ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 721 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.26 Å³/Da / Density % sol: 62.29 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 0.1 M sodium citrate, 3.2 M ammonium sulphate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.4→50 Å / Num. obs: 136613 / % possible obs: 100 % / Observed criterion σ(F): -3 / Redundancy: 11.2 % / B_iso Wilson estimate: 17.67 Å² / R_sym value: 0.081 / Net I/σ(I): 17.9
Reflection shell	Resolution: 1.4→1.5 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.99 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3HOS

3hos

Resolution: 1.4→50 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / Phase error: 20.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1954	6830	5 %	Random selection
R_work	0.1712	-	-	-
obs	0.1724	136607	99.97 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 25.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3596	0	219	721	4536

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.02	4089
X-RAY DIFFRACTION	f_angle_d	1.907	5562
X-RAY DIFFRACTION	f_dihedral_angle_d	14.294	1497
X-RAY DIFFRACTION	f_chiral_restr	0.088	565
X-RAY DIFFRACTION	f_plane_restr	0.011	685

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 (%)
1.4-1.4159	0.3508	224	0.3171	4258	X-RAY DIFFRACTION	100
1.4159-1.4326	0.3505	228	0.2992	4332	X-RAY DIFFRACTION	100
1.4326-1.45	0.3018	226	0.2872	4292	X-RAY DIFFRACTION	100
1.45-1.4684	0.2924	224	0.2686	4263	X-RAY DIFFRACTION	100
1.4684-1.4877	0.2979	228	0.2635	4322	X-RAY DIFFRACTION	100
1.4877-1.5081	0.2527	225	0.2382	4281	X-RAY DIFFRACTION	100
1.5081-1.5297	0.2679	224	0.2277	4258	X-RAY DIFFRACTION	100
1.5297-1.5525	0.2363	227	0.2259	4306	X-RAY DIFFRACTION	100
1.5525-1.5768	0.2262	226	0.2114	4304	X-RAY DIFFRACTION	100
1.5768-1.6026	0.2399	225	0.2061	4275	X-RAY DIFFRACTION	100
1.6026-1.6302	0.2508	229	0.1958	4347	X-RAY DIFFRACTION	100
1.6302-1.6599	0.209	225	0.1824	4261	X-RAY DIFFRACTION	100
1.6599-1.6918	0.2138	226	0.1804	4308	X-RAY DIFFRACTION	100
1.6918-1.7264	0.2016	227	0.1682	4305	X-RAY DIFFRACTION	100
1.7264-1.7639	0.2211	225	0.1689	4278	X-RAY DIFFRACTION	100
1.7639-1.8049	0.1938	227	0.1662	4317	X-RAY DIFFRACTION	100
1.8049-1.8501	0.2055	227	0.1646	4306	X-RAY DIFFRACTION	100
1.8501-1.9001	0.1976	228	0.1724	4329	X-RAY DIFFRACTION	100
1.9001-1.956	0.1882	227	0.1742	4316	X-RAY DIFFRACTION	100
1.956-2.0191	0.193	227	0.1697	4321	X-RAY DIFFRACTION	100
2.0191-2.0913	0.1962	227	0.1623	4310	X-RAY DIFFRACTION	100
2.0913-2.1751	0.1908	228	0.1573	4330	X-RAY DIFFRACTION	100
2.1751-2.2741	0.2047	229	0.1547	4343	X-RAY DIFFRACTION	100
2.2741-2.394	0.1669	228	0.1557	4338	X-RAY DIFFRACTION	100
2.394-2.5439	0.199	229	0.1678	4361	X-RAY DIFFRACTION	100
2.5439-2.7404	0.2076	230	0.172	4364	X-RAY DIFFRACTION	100
2.7404-3.0162	0.2045	230	0.1704	4363	X-RAY DIFFRACTION	100
3.0162-3.4526	0.1682	230	0.1561	4382	X-RAY DIFFRACTION	100
3.4526-4.3498	0.155	233	0.1357	4416	X-RAY DIFFRACTION	100
4.3498-72.9308	0.1866	241	0.18	4591	X-RAY DIFFRACTION	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	1.3141	-0.0235	0.545	3.69	-3.2452	4.4234	0.0844	0.015	-0.0266	0.0118	-0.1632	-0.1386	-0.0699	0.2443	0.0676	0.0732	0.0041	0.0005	0.1127	-0.0003	0.1628	23.4634	22.4473	-12.1976
2	5.7626	-0.082	-0.4462	3.6429	-0.2065	4.5755	0.0812	0.701	-0.6331	0.0615	-0.0851	-0.5858	0.2916	0.3804	0.0069	0.159	0.0316	-0.0659	0.1635	-0.0184	0.2656	18.4336	4.5168	-9.2856
3	7.2275	-4.8547	5.4483	3.2475	-3.6583	4.0925	-0.1532	-0.0181	0.1383	0.1538	-0.0001	-0.1112	-0.1636	0.0047	0.19	0.121	-0.0216	-0.0175	0.1139	0.0001	0.1501	-5.1612	23.9129	-16.059
4	8.2954	1.6734	5.3111	1.2314	1.6843	4.8617	-0.2444	0.4345	0.2063	-0.2967	0.0919	0.1656	-0.3652	0.2065	0.1259	0.1614	0.0245	-0.0127	0.1214	-0.0078	0.1434	-16.1019	33.5555	-24.5989
5	3.5631	-0.4581	0.6682	0.7906	-1.2085	1.8394	-0.1986	-0.3129	0.177	0.3045	0.1832	0.029	-0.1366	-0.139	0.0164	0.1423	-0	-0.0418	0.1364	-0.0032	0.1278	-2.7685	15.9339	-4.5034
6	4.0826	-2.3026	-2.4901	4.9043	6.2186	7.9451	-0.0136	-0.2476	-0.3742	0.5394	-0.2675	0.5937	0.6033	-0.5907	0.1728	0.2094	-0.0269	-0.0186	0.2499	0.0497	0.1823	-0.4122	7.8397	1.8833
7	3.0878	-0.0278	-0.196	1.3877	0.4891	2.4402	-0.0199	-0.3811	-0.033	0.1897	0.1007	-0.0209	0.1604	-0.0016	-0.057	0.1158	0.0139	-0.0426	0.1642	0.0074	0.1369	10.6882	12.2765	1.1332
8	8.1733	-2.5098	4.6108	2.0438	-0.9178	4.6678	0.1158	0.2137	0.1419	-0.1573	-0.1478	-0.0241	0.0616	0.0832	0.0813	0.1106	-0.0049	-0.0219	0.0916	0.0059	0.1085	-1.9519	15.5559	-17.9099
9	1.431	-3.0373	0.3055	7.6344	0.5709	2.0227	0.0971	-0.0587	-0.2755	0.0059	0.0464	0.5185	0.0932	-0.1305	-0.1295	0.1022	-0.0307	-0.0374	0.1427	0.0198	0.1974	-12.568	14.6419	-14.5791
10	7.2986	1.0664	3.7569	2.83	1.8164	5.7675	0.4541	0.7378	-0.4026	-0.3601	-0.242	0.1227	-0.1345	-0.0236	-0.1387	0.1972	0.0499	-0.0557	0.1982	-0.0443	0.161	5.595	5.933	-18.7248
11	6.1652	1.4579	-0.2578	7.3878	-0.4855	4.3378	0.0112	0.108	-0.2191	-0.1973	-0.0945	-0.3032	0.3622	0.2563	0.0798	0.1303	0.033	0.011	0.1331	0	0.0908	21.0521	17.941	-17.0481
12	3.1042	-0.9161	-0.6651	2.4486	-0.8232	3.3796	0.0885	0.4146	-0.0144	-0.446	-0.2155	0.1303	-0.2258	-0.5114	0.1082	0.2822	0.0695	-0.0076	0.2606	-0.0485	0.1195	-25.8052	4.1997	-59.2355
13	1.881	-1.0577	2.6261	1.9502	-1.657	4.3692	0.1016	0.165	-0.0148	-0.2016	-0.1316	0.0234	-0.0177	0.0553	0.0468	0.1451	0.0424	0.0062	0.1635	-0.0411	0.0943	-24.8798	11.4061	-39.9038
14	7.0809	1.539	5.4869	1.2572	1.2176	7.1047	0.1818	0.0539	-0.3386	0.4452	-0.0086	-0.4339	0.1975	0.2265	-0.1686	0.2229	-0.0251	-0.0867	0.1223	0.0253	0.2183	-13.3624	-4.1766	-20.3637
15	1.407	-0.7889	0.8184	1.8961	-0.0712	2.0109	0.0246	-0.1866	-0.1224	0.1459	0.0003	0.33	-0.0729	-0.368	-0.0171	0.1498	0.0524	-0.0094	0.2093	-0.0228	0.1442	-36.7202	16.1379	-35.4476
16	2.8024	-0.9591	-0.6016	1.4442	0.8017	1.104	-0.0499	0.1436	-0.3552	-0.0842	-0.1777	0.4892	-0.0111	-0.2598	0.1126	0.2033	0.0764	-0.0306	0.2505	-0.0575	0.2187	-40.0354	13.5251	-47.0865
17	0.4929	-0.1924	0.3208	1.587	-0.3263	2.1467	-0.0119	0.0031	0.0355	0.0285	-0.0842	-0.1529	-0.1047	-0.0281	0.0913	0.1513	0.0264	-0.0228	0.167	-0.012	0.1434	-21.8337	16.0786	-32.9437
18	1.1365	-0.1276	0.2438	3.6167	0.9195	1.7206	0.0229	0.1627	0.1017	-0.5611	-0.0882	-0.0148	-0.2693	-0.1062	0.0784	0.2769	0.0551	0.0292	0.1759	0.0166	0.1468	-21.4718	9.3544	-57.3518

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 7 through 27 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 28 through 40 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 41 through 58 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 59 through 80 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 81 through 104 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 105 through 123 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 124 through 166 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 167 through 182 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 183 through 200 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 201 through 212 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 213 through 230 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 7 through 28 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 29 through 58 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 59 through 80 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 81 through 123 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 124 through 166 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 167 through 212 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 213 through 230 )

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