PDB-5u91: Crystal structure of Tre/loxLTR complex

ID or keywords:

Entry

Database: PDB / ID: 5u91

Title

Crystal structure of Tre/loxLTR complex

Components

(DNA (37-MER)) x 2
Tre recombinase protein

Keywords

ISOMERASE/DNA / Cre mutant Tre recombinase / ISOMERASE-DNA complex

Function / homology

Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A /

DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha /

DNA / DNA (> 10)

Function and homology information

Biological species

synthetic construct (others)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.104 Å

Authors

Meinke, G. / Karpinski, J. / Buchholz, F. / Bohm, A.

Citation

Journal: Nucleic Acids Res. / Year: 2017
Title: Crystal structure of an engineered, HIV-specific recombinase for removal of integrated proviral DNA.
Authors: Meinke, G. / Karpinski, J. / Buchholz, F. / Bohm, A.

History

Deposition	Dec 15, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2017	Group: Database references / Refinement description / Category: citation / software Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Oct 4, 2023	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	5u91.cif.gz	677 KB	Display	PDBx/mmCIF format
PDB format	pdb5u91.ent.gz	555 KB	Display	PDB format
PDBx/mmJSON format	5u91.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/u9/5u91 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/5u91	HTTPS FTP

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Related structure data

Related structure data	1q3uS S: Starting model for refinement
Similar structure data	1nzb-d 1q3u-d 1ouq-d 1q3v-d 3c29-d 4crx-1 1pvq-1 3crx-1 1pvr-1 3c28-1 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #135 - Mar 2011 Integrase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #160 - Apr 2013 Actinomycin 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) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems 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
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Deposited unit

A: Tre recombinase protein

B: Tre recombinase protein

E: Tre recombinase protein

F: Tre recombinase protein

C: DNA (37-MER)

D: DNA (37-MER)

G: DNA (37-MER)

H: DNA (37-MER)

201 kDa, 8 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)	70.260, 193.390, 89.020
Angle α, β, γ (deg.)	90.000, 111.250, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Tre recombinase protein Mass: 38792.402 Da / Num. of mol.: 4 / Mutation: Y324F Source method: isolated from a genetically manipulated source Details: molecularly evolved from Cre recombinase / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
#2: DNA chain	DNA (37-MER) Mass: 11223.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: DNA chain	DNA (37-MER) Mass: 11547.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.9 Å³/Da / Density % sol: 57.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 10 mM sodium citrate, 25-32.5 % Peg 6000 / Temp details: room temperature

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2014
Radiation	Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 3.1→96.69 Å / Num. obs: 71563 / % possible obs: 90.7 % / Redundancy: 4.2 % / CC_1/2: 0.951 / Net I/σ(I): 3.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SCALEPACK		data scaling
PHASER		phasing
PHENIX	dev_1839	refinement
PDB_EXTRACT	3.22	data extraction
DENZO		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1Q3U

1q3u

Resolution: 3.104→82.967 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 26.95

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.253	3598	5.03 %	RANDOM
R_work	0.2091	-	-	-
obs	0.2112	71563	90.6 %	-

Solvent computation

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

Displacement parameters

B_iso max: 141.51 Å² / B_iso mean: 56.978 Å² / B_iso min: 21.4 Å²

Refinement step

Cycle: final / Resolution: 3.104→82.967 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10202	3022	0	35	13259
B_iso mean	-	-	-	29.55	-
Num. residues	-	-	-	-	1451

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	13769
X-RAY DIFFRACTION	f_angle_d	0.639	19268
X-RAY DIFFRACTION	f_chiral_restr	0.032	2166
X-RAY DIFFRACTION	f_plane_restr	0.004	1972
X-RAY DIFFRACTION	f_dihedral_angle_d	21.182	5302

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.104-3.1449	0.3465	96	0.2682	1487	1583	52
3.1449-3.188	0.3281	100	0.2695	1681	1781	58
3.188-3.2335	0.3363	110	0.2658	1906	2016	68
3.2335-3.2818	0.304	111	0.2546	2221	2332	75
3.2818-3.3331	0.241	129	0.2444	2234	2363	78
3.3331-3.3877	0.281	127	0.2214	2431	2558	85
3.3877-3.4461	0.2978	123	0.2461	2466	2589	85
3.4461-3.5088	0.2981	148	0.242	2501	2649	85
3.5088-3.5763	0.2735	155	0.2373	2623	2778	94
3.5763-3.6493	0.2773	162	0.2546	2726	2888	94
3.6493-3.7286	0.3492	113	0.2642	2803	2916	96
3.7286-3.8154	0.2979	132	0.2594	2871	3003	98
3.8154-3.9108	0.3591	132	0.2882	2805	2937	97
3.9108-4.0165	0.3146	122	0.2386	2868	2990	99
4.0165-4.1347	0.2613	154	0.2076	2865	3019	98
4.1347-4.2681	0.2485	157	0.1963	2829	2986	99
4.2681-4.4207	0.2535	130	0.1869	2859	2989	98
4.4207-4.5977	0.2033	168	0.1965	2819	2987	99
4.5977-4.8069	0.2456	129	0.1899	2859	2988	99
4.8069-5.0603	0.2078	143	0.1897	2915	3058	99
5.0603-5.3773	0.2347	158	0.1891	2864	3022	100
5.3773-5.7924	0.2752	161	0.1987	2863	3024	100
5.7924-6.3751	0.2326	182	0.1903	2874	3056	100
6.3751-7.2971	0.2372	174	0.1869	2836	3010	100
7.2971-9.1917	0.1669	156	0.1531	2886	3042	100
9.1917-82.9968	0.1827	126	0.1553	2873	2999	99

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	1.3083	-0.1322	0.5533	0.7229	0.2009	2.0107	-0.1051	-0.0076	-0.1202	-0.0106	0.1723	0.0566	-0.2793	-0.4622	0	0.2727	0.1272	0.0316	0.3779	0.0391	0.4734	81.5689	-12.6749	344.0257
2	0.4505	0.1692	-1.0176	0.5815	0.6523	1.3871	-0.1105	-0.1495	0.1915	-0.0236	0.0009	-0.1965	-0.3585	0.0046	-0.002	0.5305	0.0121	-0.0153	0.3552	-0.0431	0.4557	103.8383	-9.624	349.922
3	2.5075	-0.4063	-0.625	1.3849	-0.3357	0.9594	-0.0682	0.0067	0.0469	0.013	-0.0109	0.1622	0.1489	-0.2146	-0.0072	0.1717	0.0392	0.0261	0.3925	0.0241	0.2997	86.8323	-42.4919	359.9434
4	0.9893	0.121	-0.1695	2.1808	0.4834	1.2309	0.0632	0.0002	0.0692	-0.1647	-0.0559	-0.1178	0.1766	0.1517	0.0001	0.1545	-0.0064	-0.0146	0.3492	0.067	0.3292	111.2918	-46.2808	351.7649
5	1.6016	0.0397	0.24	1.5302	0.8316	0.3746	0.2576	-0.2012	-0.4102	0.2825	-0.1153	0.5054	0.0486	-0.0029	0.0128	0.4429	0.0184	0.057	0.4233	0.0698	0.2547	96.1143	-40.6846	358.8359
6	3.5242	3.0784	2.8872	3.5283	4.3112	6.5936	0.237	-1.1001	0.6052	0.3234	-0.9195	0.3127	-1.1448	-1.3216	0.1802	1.2609	0.0997	-0.1866	0.4254	-0.0715	1.0426	87.3295	10.0978	358.216
7	0.6686	-0.0733	0.4343	0.0249	0.2607	0.9993	0.2558	-0.504	0.1589	0.4282	-0.5751	0.0784	-0.5745	-0.7032	-0.0084	0.984	0.1399	-0.0648	0.6068	-0.1637	0.5883	87.4081	2.0325	351.913
8	1.8167	0.6902	-0.4241	0.9573	0.326	0.9457	0.0475	-0.0508	-0.1071	0.8831	-0.0822	0.3793	-0.0533	0.127	0.0026	0.569	0.1001	0.0066	0.459	-0.0107	0.2833	97.7651	-49.247	362.1077
9	-0.0013	-0.0232	0.0022	0.0581	0.083	0.0658	-0.6903	0.3799	-0.0445	-0.1403	0.9894	0.4107	0.6049	-0.625	-0	0.7922	-0.0087	0.0577	0.7127	0.0459	0.9332	69.6079	-62.0055	316.5945
10	1.0735	0.7165	-0.586	1.8532	0.8737	1.861	-0.1274	-0.0018	0.1563	0.0615	0.024	0.1869	0.431	-0.4431	-0.0053	0.3786	-0.1273	0.0425	0.4362	0.0041	0.353	82.2728	-62.811	331.8002
11	1.2684	0.5766	0.533	1.2515	0.1386	2.1771	-0.1229	0.1271	-0.2731	-0.2817	0.1408	-0.1614	0.3111	0.1098	0.0001	0.3507	0.0146	0.1009	0.3588	-0.0422	0.3812	110.2342	-57.525	311.9523
12	2.5851	0.6915	0.6193	1.8963	0.4338	0.822	-0.118	-0.0532	0.0564	-0.0353	0.1237	0.3462	-0.1047	-0.2234	0.0005	0.4107	-0.0259	-0.0173	0.4418	0.0641	0.4076	78.532	-34.2759	308.7914
13	1.6051	-0.1113	0.1653	2.5558	0.0051	1.4643	-0.159	0.1257	0.0845	-0.1591	0.1261	-0.0581	-0.5077	0.0837	-0.0021	0.515	-0.0817	0.0327	0.3244	0.0905	0.2896	99.8408	-20.1258	310.4079
14	0.5249	0.0568	-0.1387	0.0249	0.0164	0.2565	-0.0153	-0.3034	0.7334	-0.9421	-0.0166	1.2655	-0.6066	0.1771	-0.1413	1.0116	-0.1954	-0.1776	0.5508	0.2303	0.7131	83.6596	-12.7826	294.2114
15	0.3832	-0.0271	-0.0136	0.2216	0.2278	0.1116	0.1946	0.1168	-0.4537	0.5364	-0.1115	0.4464	0.2935	-0.1347	0.0134	0.6265	-0.1096	0.042	0.4108	0.0489	0.3726	86.8935	-39.7827	318.9487
16	0.6256	-0.1595	0.5044	0.0503	-0.0873	0.3205	-0.1073	0.4163	-0.448	-0.1323	0.0252	-0.5231	0.8559	-0.2147	0.0213	1.0425	-0.1244	0.1501	0.4279	-0.1142	0.5591	98.9248	-74.5868	311.4619
17	2.1317	0.0474	0.0545	0.2776	-0.7666	2.1843	-0.0966	0.5871	-1.3326	-0.0879	-0.3343	0.2656	1.6791	-1.1565	1.4813	1.25	-0.146	0.1521	0.556	-0.2437	0.6983	103.8032	-82.9419	305.9066
18	0.1822	-0.1475	0.37	0.9172	0.0155	2.8002	-0.0594	0.6183	0.7915	0.5743	-0.387	0.2185	0.1283	0.3868	0.1098	0.5254	-0.1292	-0.0121	0.4589	0.1375	0.7127	92.5416	-60.4931	321.5009
19	0.9388	-0.3003	0.573	0.6129	0.7853	1.8807	-0.0579	0.3125	0.1955	-0.8135	0.2874	0.8538	-0.1938	-0.1821	-0.0057	0.7629	0.0292	-0.1015	0.5587	0.0768	0.5636	83.4818	-20.7527	302.9569

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 12:178)	A	12 - 178
2	X-RAY DIFFRACTION	2	(chain A and resid 179:340)	A	179 - 340
3	X-RAY DIFFRACTION	3	(chain B and resid 15:157)	B	15 - 157
4	X-RAY DIFFRACTION	4	(chain B and resid 158:341)	B	158 - 341
5	X-RAY DIFFRACTION	5	(chain C and resid 100:127)	C	100 - 127
6	X-RAY DIFFRACTION	6	(chain C and resid 128:136)	C	128 - 136
7	X-RAY DIFFRACTION	7	(chain D and resid 100:116)	D	100 - 116
8	X-RAY DIFFRACTION	8	(chain D and resid 117:136)	D	117 - 136
9	X-RAY DIFFRACTION	9	(chain E and resid 13:34)	E	13 - 34
10	X-RAY DIFFRACTION	10	(chain E and resid 35:133)	E	35 - 133
11	X-RAY DIFFRACTION	11	(chain E and resid 134:341)	E	134 - 341
12	X-RAY DIFFRACTION	12	(chain F and resid 10:156)	F	22 - 156
13	X-RAY DIFFRACTION	13	(chain F and resid 157:341)	F	157 - 341
14	X-RAY DIFFRACTION	14	(chain G and resid 100:112)	G	100 - 112
15	X-RAY DIFFRACTION	15	(chain G and resid 113:122)	G	113 - 122
16	X-RAY DIFFRACTION	16	(chain G and resid 123:136)	G	123 - 136
17	X-RAY DIFFRACTION	17	(chain H and resid 100:108)	H	100 - 108
18	X-RAY DIFFRACTION	18	(chain H and resid 109:118)	H	109 - 118
19	X-RAY DIFFRACTION	19	(chain H and resid 119:136)	H	119 - 136

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

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
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