PDB-5c6k: Bacteriophage P2 integrase catalytic domain

ID or keywords:

Entry

Database: PDB / ID: 5c6k

Title

Bacteriophage P2 integrase catalytic domain

Components

Integrase

Keywords

HYDROLASE /

Integrase / tyrosine recombinase / integration /

site-specific recombination

Function / homology

Function and homology information

DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency /

Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases /

transferase activity / DNA recombination /

Hydrolases; Acting on ester bonds /

hydrolase activity / symbiont entry into host cell /

Biological species

Enterobacteria phage P2 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Skaar, K. / Claesson, M. / Odegrip, R. / Eriksson, J. / Hogbom, M. / Haggard-Ljungquist, E. / Stenmark, P.

Funding support

Sweden, 3items

Citation

Journal: Febs Lett. / Year: 2015
Title: Crystal structure of the bacteriophage P2 integrase catalytic domain.
Authors: Skaar, K. / Claesson, M. / Odegrip, R. / Hogbom, M. / Haggard-Ljungquist, E. / Stenmark, P.

History

Deposition	Jun 23, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Oct 21, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 2, 2015	Group: Database references
Revision 1.2	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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PDBx/mmCIF format	5c6k.cif.gz	152.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5c6k.ent.gz	119.7 KB	Display	PDB format
PDBx/mmJSON format	5c6k.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/c6/5c6k ftp://data.pdbj.org/pub/pdb/validation_reports/c6/5c6k	HTTPS FTP

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Related structure data

Related structure data	5dorC 1aihS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5dor-1 5dor-2 2yox-d 1aih-2 2i2s-d 1mmp-d 6hse-2 3sit-d 1red-d 1cjf-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	#135 - Mar 2011 Integrase similarity (1) #84 - Dec 2006 Transposase similarity (7) #73 - Jan 2006 Topoisomerase similarity (1) #160 - Apr 2013 Actinomycin similarity (1)

Deposited unit

A: Integrase

B: Integrase

66.1 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)	215.004, 54.420, 38.610
Angle α, β, γ (deg.)	90.00, 97.33, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Integrase / Mass: 33026.023 Da / Num. of mol.: 2 / Fragment: UNP residues 46-337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P2 (virus) / Gene: int / Plasmid: pET8c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P36932
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 280 / 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 grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium nitrate, 0.1 M BisTris propane pH7.5, 20 % (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.9→38.29 Å / Num. obs: 34250 / % possible obs: 97.9 % / Redundancy: 4.1 % / R_merge(I) obs: 0.084 / Net I/σ(I): 11.6
Reflection shell	Resolution: 1.9→1.94 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.4 / % possible all: 96.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1AIH

1aih

Resolution: 1.9→35.541 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2009	1720	5.03 %
R_work	0.1714	-	-
obs	0.1729	34216	97.46 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→35.541 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2599	0	0	280	2879

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2650
X-RAY DIFFRACTION	f_angle_d	1.011	3581
X-RAY DIFFRACTION	f_dihedral_angle_d	13.892	991
X-RAY DIFFRACTION	f_chiral_restr	0.04	408
X-RAY DIFFRACTION	f_plane_restr	0.005	460

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 (%)
1.9-1.9559	0.2158	118	0.2311	2671	X-RAY DIFFRACTION	96
1.9559-2.019	0.2749	113	0.2227	2710	X-RAY DIFFRACTION	97
2.019-2.0912	0.2444	156	0.1981	2697	X-RAY DIFFRACTION	98
2.0912-2.1749	0.2335	155	0.1827	2684	X-RAY DIFFRACTION	98
2.1749-2.2739	0.2381	140	0.2044	2680	X-RAY DIFFRACTION	97
2.2739-2.3937	0.2215	128	0.1743	2722	X-RAY DIFFRACTION	98
2.3937-2.5437	0.1947	146	0.1721	2701	X-RAY DIFFRACTION	98
2.5437-2.74	0.2089	140	0.1749	2735	X-RAY DIFFRACTION	98
2.74-3.0156	0.233	134	0.1737	2740	X-RAY DIFFRACTION	98
3.0156-3.4517	0.2162	155	0.1691	2720	X-RAY DIFFRACTION	98
3.4517-4.3475	0.1659	165	0.1371	2686	X-RAY DIFFRACTION	97
4.3475-35.5476	0.1635	170	0.1573	2750	X-RAY DIFFRACTION	97

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	2.7324	2.0288	1.3473	3.9797	1.9736	6.9127	0.1023	0.6503	0.2857	-0.2845	0.0344	0.0545	-0.376	0.1805	-0.0987	0.2658	0.0132	0.0115	0.1298	0.0061	0.1055	-58.1117	-30.3563	-1.3566
2	2.8037	0.2523	0.7288	2.0285	1.0502	5.8343	-0.0506	-0.1439	-0.0745	0.2136	-0.017	0.0178	0.0609	-0.2779	0.0736	0.147	0.0091	0.0061	0.0629	-0.0028	0.1294	-62.7463	-36.4808	14.5496
3	2.1199	-1.1094	1.5793	6.288	-1.0743	3.4342	-0.1394	-0.0944	0.186	0.1408	0.0205	-0.1827	0.0098	-0.2436	0.1213	0.1186	-0.0172	0.0534	0.083	-0.0014	0.0664	-58.873	-35.4591	18.0578
4	5.6152	0.7136	-4.4311	1.5875	-0.9707	7.0156	-0.1333	0.0203	-0.0735	-0.1198	0.0571	0.1361	0.3288	-0.5612	0.0468	0.1392	-0.0381	-0.0254	0.1462	-0.0177	0.1745	-67.0246	-40.4271	5.8242
5	3.2534	0.7518	0.9877	1.1172	-0.0944	3.3684	-0.0027	0.1971	-0.1433	-0.0686	0.0255	-0.1408	0.0981	0.2107	-0.0431	0.1744	0.0142	0.0239	0.0642	-0.0014	0.151	-46.9834	-34.5105	8.8274
6	9.4226	6.1429	4.3616	6.3375	1.7647	2.998	-0.5254	0.2789	0.4633	-0.2449	0.2861	0.2339	-0.3901	0.1265	0.2759	0.1784	0.0293	-0.0094	0.2108	0.0201	0.2568	-30.9073	-14.9232	16.5163
7	6.1744	4.3755	-1.5081	6.1154	0.2761	5.8038	0.3667	-0.9836	0.124	0.4494	-0.377	-0.1051	-0.2018	-0.117	-0.0102	0.2773	0.0182	-0.0535	0.4421	-0.0641	0.1786	-23.3874	-15.558	33.5659
8	7.435	0.5954	1.5664	2.2545	-0.5874	1.7689	-0.0463	-0.1806	-0.0413	0.261	-0.0113	-0.2799	0.0413	0.7527	-0.0101	0.1341	0.0017	-0.0286	0.4015	0.0103	0.1818	-16.2891	-18.3895	23.1184
9	8.9837	2.8511	-3.7154	6.6841	-0.0828	5.692	-0.1673	1.0635	-0.1095	-0.2936	0.2104	-0.2856	0.2457	0.364	0.0199	0.1976	0.0333	0.0103	0.5253	-0.0214	0.2508	-14.9755	-17.4758	10.813
10	8.5376	0.4366	-0.7132	2.864	1.4497	8.3422	-0.2074	0.31	-1.1725	-0.9296	0.3744	-0.108	1.0957	0.5412	-0.0888	0.3287	0.0689	0.0272	0.4145	-0.0506	0.3222	-18.4151	-25.1939	12.0521
11	2.6828	-1.7709	-0.6732	3.4117	5.0623	9.6938	0.2414	0.568	1.1545	-0.0388	-0.3334	-1.4229	-0.8094	0.8825	0.1154	0.2884	-0.0746	-0.0609	0.4331	0.1705	0.5214	-17.1939	-7.8646	16.6507
12	6.0179	-0.3513	-1.9501	3.5364	-0.8921	4.5259	0.1515	-0.1249	0.5844	-0.0344	0.086	-0.1143	-0.3938	0.253	-0.0647	0.171	-0.0268	-0.0134	0.6239	-0.0164	0.364	-7.0419	-13.1717	18.5141
13	5.1906	-1.8166	-2.4351	2.6783	2.1536	3.4687	-0.1364	-1.0165	-0.3217	0.6447	-0.2433	0.0456	0.1334	0.3072	0.1615	0.2597	0.025	-0.1156	0.7501	0.0799	0.2571	-13.6102	-21.1255	35.6743
14	0.9691	0.7987	-1.449	1.2357	0.448	6.7214	-0.0689	-0.8492	-0.7613	0.5767	0.069	-0.0554	1.5382	0.1876	0.0629	0.5389	0.1013	-0.0238	0.7947	0.1356	0.3193	-19.7335	-27.8349	34.479
15	2.0295	0.1354	1.5272	4.6914	-1.2162	5.5877	0.1067	-0.2482	-0.3488	0.2986	-0.0318	-0.0714	-0.1689	0.031	-0.0947	0.1229	0.0239	-0.0015	0.2387	-0.0155	0.1546	-28.7833	-22.8929	24.7087
16	5.5565	-4.4609	0.0044	9.3618	4.5002	7.1479	0.0429	0.4419	-0.1406	-0.2699	-0.0394	0.1517	0.0641	-0.1551	-0.0743	0.1285	-0.0083	0.0115	0.2128	0.0089	0.1491	-31.9394	-25.2412	15.9387
17	7.9387	0.6267	1.3657	0.3464	-0.6016	2.0813	0.0356	-0.3561	-0.4118	0.0174	-0.0664	-0.1124	0.0192	0.2421	0.0611	0.1821	-0.0092	0.002	0.0951	0.0178	0.1812	-38.6486	-29.6285	20.5915
18	3.2741	0.3259	-2.7804	1.9955	-1.8079	3.5511	-0.2143	0.6131	0.9028	-0.6307	0.0505	0.2088	-0.235	-0.3918	0.015	0.3442	-0.0073	-0.0426	0.1425	0.0401	0.2244	-59.5781	-22.5436	5.3075

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 162 through 178 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 179 through 213 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 214 through 234 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 235 through 258 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 259 through 307 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 308 through 326 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 163 through 178 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 179 through 199 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 200 through 213 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 214 through 227 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 228 through 235 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 236 through 247 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 248 through 258 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 259 through 269 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 270 through 281 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 282 through 293 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 294 through 317 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 318 through 330 )

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