PDB-5jjv: Crystal structure of XerH site-specific recombinase bound to pali...

ID or keywords:

Entry

Database: PDB / ID: 5jjv

Title

Crystal structure of XerH site-specific recombinase bound to palindromic difH substrate: post-cleavage complex

Components

DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')
DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')
Tyrosine recombinase XerH

Keywords

RECOMBINATION / Xer / tyrosine recombinase / site-specific recombinase / chromosome dimer resolution /

cell cycle

Function / homology

Function and homology information

tyrosine-based site-specific recombinase activity /

chromosome segregation / DNA recombination /

cell division /

DNA binding /

cytoplasm
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Helicobacter pylori 26695 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.4 Å

Authors

Bebel, A. / Barabas, O.

Citation

Journal: Elife / Year: 2016
Title: Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending.
Authors: Bebel, A. / Karaca, E. / Kumar, B. / Stark, W.M. / Barabas, O.

History

Deposition	Apr 25, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 11, 2017	Group: Database references
Revision 1.2	Sep 19, 2018	Group: Advisory / Data collection / Database references Category: citation_author / diffrn_radiation_wavelength / pdbx_unobs_or_zero_occ_atoms Item: _citation_author.identifier_ORCID / _diffrn_radiation_wavelength.wavelength

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5jjv.cif.gz	357.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5jjv.ent.gz	300.5 KB	Display	PDB format
PDBx/mmJSON format	5jjv.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/jj/5jjv ftp://data.pdbj.org/pub/pdb/validation_reports/jj/5jjv	HTTPS FTP

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Related structure data

Related structure data	5jk0C C: citing same article (ref.)
Similar structure data	5jk0-d 3vo0-3 3ndy-d 1ne7-d 9579 7apr-2 6l8t-d 4k81-d 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

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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) #172 - Apr 2014 RecA and Rad51 similarity (1) #253 - Jan 2021 Expressome similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #84 - Dec 2006 Transposase similarity (8) #150 - Jun 2012 Sliding Clamps similarity (1) #135 - Mar 2011 Integrase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (2) #139 - Jul 2011 DNA Methyltransferase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #160 - Apr 2013 Actinomycin similarity (2) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #39 - Mar 2003 lac Repressor 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

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Deposited unit

A: Tyrosine recombinase XerH

B: Tyrosine recombinase XerH

C: DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')

D: DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')

E: DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')

F: DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')

hetero molecules

103 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tyrosine recombinase XerH

B: Tyrosine recombinase XerH

C: DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')

D: DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')

E: DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')

F: DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')

hetero molecules

A: Tyrosine recombinase XerH

B: Tyrosine recombinase XerH

C: DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')

D: DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')

E: DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')

F: DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')

hetero molecules

defined by author&software
206 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.380, 115.220, 235.200
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-563- HOH
2	1	B-539- HOH
3	1	B-556- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Tyrosine recombinase XerH Mass: 42000.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: xerH, HP_0675 / Plasmid: pETM-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25386

#1: Protein

Tyrosine recombinase XerH

Mass: 42000.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: xerH, HP_0675 / Plasmid: pETM-28 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25386

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain	DNA (5'-D(TPAPGPTPTPAPTPGPAPAPAPAPC)-3') Mass: 3998.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695* (bacteria) / Production host: Escherichia coli (E. coli)
#3: DNA chain	DNA (5'-D(TPGPCPAPGPTPTPTPTPCPAPTPAPAPCPTPA)-3') Mass: 5176.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695* (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 163 molecules

#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.86	56.98
2

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
279.15	1	vapor diffusion	6.5	0.1 M HEPES 0.2M magnesium chloride 37% PEG 400
279.15	2	vapor diffusion	6.3	0.1 M HEPES 0.2M magnesium chloride 39% PEG 400

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ESRF	ID29	1	0.97908
SYNCHROTRON	ESRF	ID29	2	0.97908

Detector

Type	ID	Detector	Date
DECTRIS PILATUS3 6M	1	PIXEL	Apr 12, 2014
DECTRIS PILATUS3 6M	2	PIXEL	Apr 12, 2014

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97908	1
2	0.97908	1

Reflection

Entry-ID: 5JJV / R_sym value: 0.097

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	CC_1/2	Diffraction-ID	Net I/σ(I)
2.4-46.963	46216	99.86	8.1	0.999	1	14.9
3.15-47.04	37960	97.2	2.7	0.994	2	11.17

Reflection shell

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.4-2.49	8.2	1.51	1	99.5
3.15-3.2	2.6	1.89	2	96.2

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.4→46.963 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.97

	R_factor	Num. reflection	% reflection
R_free	0.2203	2310	5 %
R_work	0.1949	-	-
obs	0.1962	46216	99.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→46.963 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5574	1202	55	153	6984

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7060
X-RAY DIFFRACTION	f_angle_d	0.545	9773
X-RAY DIFFRACTION	f_dihedral_angle_d	17.987	2661
X-RAY DIFFRACTION	f_chiral_restr	0.021	1110
X-RAY DIFFRACTION	f_plane_restr	0.002	1035

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 (%)
2.4-2.4522	0.3255	141	0.3217	2681	X-RAY DIFFRACTION	99
2.4522-2.5092	0.3677	142	0.3065	2711	X-RAY DIFFRACTION	100
2.5092-2.572	0.3601	143	0.2984	2711	X-RAY DIFFRACTION	100
2.572-2.6415	0.3377	142	0.2899	2700	X-RAY DIFFRACTION	100
2.6415-2.7192	0.2796	143	0.2856	2714	X-RAY DIFFRACTION	100
2.7192-2.807	0.3145	144	0.2703	2735	X-RAY DIFFRACTION	100
2.807-2.9073	0.3086	142	0.2751	2705	X-RAY DIFFRACTION	100
2.9073-3.0237	0.3477	144	0.2618	2726	X-RAY DIFFRACTION	100
3.0237-3.1613	0.3254	143	0.2532	2730	X-RAY DIFFRACTION	100
3.1613-3.3279	0.2483	145	0.2339	2749	X-RAY DIFFRACTION	100
3.3279-3.5363	0.2314	145	0.1977	2746	X-RAY DIFFRACTION	100
3.5363-3.8093	0.2136	143	0.1868	2735	X-RAY DIFFRACTION	100
3.8093-4.1924	0.1773	146	0.1578	2766	X-RAY DIFFRACTION	100
4.1924-4.7985	0.1642	146	0.1484	2781	X-RAY DIFFRACTION	100
4.7985-6.0436	0.1733	148	0.1647	2798	X-RAY DIFFRACTION	100
6.0436-46.9722	0.1694	153	0.1544	2918	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	2.6112	-0.7583	-0.5018	1.5744	0.5199	4.8306	0.1148	0.5151	0.1606	-0.4589	-0.1586	0.3064	-0.2703	-0.6015	0.0286	0.7309	0.0521	-0.1906	0.6927	0.096	0.501	60.6964	13.7076	65.3189
2	2.8281	0.1559	0.1698	4.2541	1.978	4.2398	0.0313	0.4425	-0.0824	-0.682	0.0093	-0.0893	-0.1975	0.1573	-0.0546	0.6968	0.0274	-0.011	0.6697	0.1543	0.4335	76.2091	12.0668	65.2625
3	8.648	-2.5311	-1.7614	6.0305	1.0264	2.8945	0.0993	0.2355	0.38	0.21	0.0703	-0.0018	-0.5733	-0.0175	-0.2744	0.4288	-0.0159	-0.0902	0.47	0.047	0.3838	65.3746	21.3951	102.0838
4	2.5062	0.4684	0.39	2.5022	-0.514	2.0619	0.0621	0.0169	0.197	-0.0143	0.0223	0.4164	-0.0835	-0.4417	-0.0831	0.3378	0.0336	-0.0073	0.5505	0.0489	0.3895	55.1998	13.0921	100.7876
5	9.7888	7.3239	7.0518	7.1073	5.5408	5.7806	0.2667	-0.211	-0.6194	0.3522	0.2035	-0.4929	-0.1581	0.0261	-0.5376	0.4468	0.0372	0.0451	0.5484	0.0461	0.4427	83.0771	10.6197	104.6514
6	2.1643	-0.4064	-0.2556	2.3792	0.345	5.6693	0.0148	0.276	0.3323	-0.7162	0.0732	-0.2803	-0.4793	0.0372	-0.1007	0.8516	-0.1116	0.1479	0.586	0.1276	0.5196	95.8563	25.046	65.5924
7	2.105	0.6392	1.8517	2.3227	1.4156	6.2997	0.2413	0.2478	-0.0659	-0.646	-0.1018	-0.3727	0.6885	0.6793	-0.1307	0.7354	-0.0154	0.2149	0.6003	0.0063	0.5992	105.0466	12.6728	67.9965
8	2.917	0.4583	-0.5938	3.517	-0.3056	2.5503	0.1148	-0.079	0.4005	-0.0186	0.0784	-0.285	-0.5826	0.1939	-0.1804	0.5139	-0.0741	0.0636	0.456	-0.0151	0.3903	93.9444	28.0468	102.4235
9	5.8621	-5.5468	2.0073	5.3226	-1.6463	1.701	-0.0966	0.0133	0.2668	-0.0177	-0.0169	-0.3563	0.0221	0.0496	0.0852	0.4563	-0.0742	0.0463	0.6457	-0.0346	0.4795	101.2513	4.1102	102.5742
10	2.5154	-2.4007	-2.6552	6.4881	-0.7457	5.2176	0.2624	0.0861	0.4791	-1.0953	0.0013	-0.6517	-0.8492	0.5205	-0.3385	0.7489	-0.2435	0.0455	0.6581	0.028	0.7291	101.6032	31.8357	86.2819
11	2.7567	-4.2189	4.3595	6.436	-6.6641	6.8741	-0.5323	1.926	2.7531	1.1063	-0.0782	-0.0168	-1.2794	0.669	0.591	1.0456	-0.0637	-0.0556	0.6833	0.366	1.6523	100.2344	3.9325	80.9684
12	5.2826	2.7189	0.4045	8.7849	-0.973	3.5603	0.2553	0.0425	0.6312	-0.0367	-0.0482	-0.7157	-1.1657	0.5488	-0.1184	0.7831	-0.1379	0.2159	0.5486	0.0575	0.5741	101.6154	32.6772	85.7339
13	7.5273	-2.9856	-5.5518	5.1932	4.4328	5.3367	0.1543	0.7562	0.7402	-0.2761	-0.5545	-0.1487	-1.4593	-0.7441	0.511	0.7892	0.2918	-0.0256	0.8699	0.1409	0.8485	46.3467	27.5881	90.0405
14	7.0508	-0.8567	-0.1995	3.453	-0.3209	2.8572	0.0172	0.5929	0.1124	-0.0365	0.115	0.7623	-0.5175	-0.5177	-0.0881	0.4766	0.079	-0.0405	0.5643	0.0845	0.4581	64.3349	19.5199	82.4912
15	4.6439	2.8727	-3.0276	7.1635	4.016	8.4392	-0.334	-0.1457	-0.6955	0.3757	0.1458	-0.3564	0.8563	0.3032	0.2384	0.6572	0.0985	-0.1048	0.6089	0.1915	0.3575	69.7744	8.104	82.6446
16	3.9574	-5.5854	0.6917	8.3146	-0.4151	8.67	-0.8053	0.1994	0.9085	0.2885	0.5404	0.9416	-1.3706	-1.713	0.2292	0.8749	0.2301	-0.1092	0.9259	0.2269	0.8719	51.9897	31.7889	84.8319

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 88 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 89 through 162 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 163 through 196 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 197 through 337 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 338 through 361 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 0 through 92 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 93 through 176 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 177 through 323 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 324 through 361 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 13 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 14 through 18 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 19 through 30 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 1 through 5 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 6 through 13 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 14 through 23 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 24 through 30 )

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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Protein , 1 types, 2 molecules AB

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DNA chain , 2 types, 4 molecules CEDF

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Non-polymers , 3 types, 163 molecules

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-Protein , 1 types, 2 molecules AB

-DNA chain , 2 types, 4 molecules CEDF

-Non-polymers , 3 types, 163 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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This page

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This web site

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Open data

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Basic information

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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

-
DNA chain , 2 types, 4 molecules CEDF

-
Non-polymers , 3 types, 163 molecules

-
Experimental details

-
Experiment

-
Sample preparation

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Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi