PDB-4e0y: Protelomerase tela covalently complexed with mutated substrate DNA

ID or keywords:

Entry

Database: PDB / ID: 4e0y

Title

Protelomerase tela covalently complexed with mutated substrate DNA

Components

DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')
DNA (5'-D(*CP*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')
ProtelomeraseTelomere resolvase

Keywords

DNA BINDING PROTEIN/DNA / PROTELEMORASE / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

Helix Hairpins - #1780 /

Telomere resolvase / Telomere resolvase ResT / Telomere resolvase ResT superfamily / Telomere resolvase ResT/TelK catalytic domain / hpI Integrase; Chain A / Helix Hairpins / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology

Biological species

Agrobacterium tumefaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Shi, K. / Aihara, H.

Citation

Journal: Plos Biol. / Year: 2013
Title: An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation.
Authors: Shi, K. / Huang, W.M. / Aihara, H.

History

Deposition	Mar 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 13, 2013	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4e0y.cif.gz	181.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4e0y.ent.gz	148.9 KB	Display	PDB format
PDBx/mmJSON format	4e0y.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/e0/4e0y ftp://data.pdbj.org/pub/pdb/validation_reports/e0/4e0y	HTTPS FTP

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Related structure data

Related structure data	4dwpC 4e0gC 4e0jC 4e0pC 4e0zC 4e10C C: citing same article (ref.)
Similar structure data	4e10-1 4nym-d 1xd2-d 6d59-d 4e0g-1 7kfz-d 6cur-d 6d5l-d 6bvi-d 6d55-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 - 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
TATA-Binding Protein
similarity (1)
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Thymine Dimers
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DNA Helicase
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Estrogen Receptor
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similarity (1)
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#240 - Dec 2019
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Twenty Years of Molecules
similarity (1)

Deposited unit

A: Protelomerase

C: DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')

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

hetero molecules

63.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protelomerase

C: DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')

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

hetero molecules

A: Protelomerase

C: DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')

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

hetero molecules

defined by author&software
126 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.984, 119.442, 56.922
Angle α, β, γ (deg.)	90.00, 112.42, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 1 molecules A

#1: Protein	Protelomerase / Telomere resolvase Mass: 52648.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: telA, Atu2523 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CWV1

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain	DNA (5'-D(CPAPTPAPAPTPAPAPCPAPAPTPAPT)-3') Mass: 4255.832 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain	DNA (5'-D(CPCPAPTPGPAPTPAPTPTPGPTPTPAPTPTPAPTPG)-3') Mass: 5824.793 Da / Num. of mol.: 1 / Source method*: obtained synthetically

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Non-polymers , 3 types, 138 molecules

#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-DT / THYMIDINE-5'-MONOPHOSPHATE / Thymidine monophosphate Type: DNA linking / Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₂O₈P / Comment: dTMP*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.93 Å³/Da / Density % sol: 58.02 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 5% (w/v) PEG 4000, 10mM Tris-HCl, 300mM NaCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 96 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2010
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. all: 21996 / Num. obs: 21996 / % possible obs: 77.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→40.082 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 33.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2698	1120	5.1 %
R_work	0.2159	-	-
obs	0.2187	21975	77.69 %
all	-	21975	-

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.388 Å² / k_sol: 0.335 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.3904 Å²	-0 Å²	2.9442 Å²
2-	-	3.9598 Å²	0 Å²
3-	-	-	-7.3502 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→40.082 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2528	593	23	136	3280

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3315
X-RAY DIFFRACTION	f_angle_d	0.857	4616
X-RAY DIFFRACTION	f_dihedral_angle_d	19.632	1284
X-RAY DIFFRACTION	f_chiral_restr	0.05	505
X-RAY DIFFRACTION	f_plane_restr	0.003	490

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 (%)
2.4-2.5092	0.3671	73	0.2742	1301	X-RAY DIFFRACTION	39
2.5092-2.6415	0.3303	76	0.2726	1730	X-RAY DIFFRACTION	51
2.6415-2.807	0.3455	103	0.2939	2160	X-RAY DIFFRACTION	64
2.807-3.0236	0.3225	162	0.3018	2627	X-RAY DIFFRACTION	79
3.0236-3.3278	0.3212	174	0.2568	3123	X-RAY DIFFRACTION	94
3.3278-3.809	0.2964	195	0.2085	3308	X-RAY DIFFRACTION	98
3.809-4.7977	0.2165	169	0.1677	3278	X-RAY DIFFRACTION	98
4.7977-40.088	0.219	168	0.1918	3328	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	8.9326	-2.2188	2.4338	2.7925	-0.0576	3.3695	-0.0325	0.4256	-0.2185	-0.037	0.0603	0.0381	0.108	0.3099	-0.0412	0.2614	0.0688	0.0144	0.4632	-0.0031	1.2632	31.1659	-32.2713	-1.4324
2	1.4176	3.031	2.0438	6.482	4.3222	4.6697	-0.1906	0.0919	-1.1605	-0.0656	0.5967	-2.3042	0.2872	1.4831	-0.4136	0.6152	-0.0325	-0.2362	0.8544	-0.0827	1.7425	42.8244	-23.216	9.501
3	5.6454	-4.1483	3.2604	6.355	1.6516	6.8339	-0.0933	-0.1011	0.044	0.7173	0.3508	-0.6166	0.1738	0.342	-0.2078	0.4376	0.0781	-0.2693	0.3871	0.1425	1.0343	31.7041	-26.7501	12.4621
4	3.9884	-0.9956	-0.2203	5.6535	0.7038	0.9451	0.0621	0.0741	-0.6505	0.0323	-0.0295	0.1653	0.1058	-0.1241	-0.1136	0.2606	0.0806	-0.1574	0.1858	0.0001	1.1146	23.0768	-41.0863	2.6544
5	2.4701	-3.4163	-0.6309	5.9076	1.8151	4.0437	-0.2885	-0.1451	-0.1911	1.0066	0.4254	-0.1239	0.0647	-0.0059	-0.124	0.4498	0.034	-0.0285	0.3021	0.1526	1.2398	17.7896	-37.6049	9.7406
6	3.8675	-0.6177	1.708	8.3081	4.9941	4.1336	-0.4053	-1.2498	-0.8258	1.4671	0.3531	-0.0593	1.0702	0.4073	0.0368	0.5343	0.0569	-0.189	0.4227	0.2737	0.8195	16.0767	-24.3356	15.2743
7	0.5164	0.0244	-0.0942	5.1682	0.4551	3.5826	0.019	-0.0693	0.4124	0.4726	0.1477	-1.266	-0.3474	0.3269	-0.1427	0.3322	0.0543	-0.0549	0.1109	-0.0023	0.6379	18.901	-24.9125	6.6772
8	0.5234	0.0114	-0.1465	6.5175	0.9458	1.4224	0.1097	0.0958	-0.2366	-0.527	0.0273	0.1105	0.0169	-0.0623	-0.044	0.2874	-0.0262	-0.1564	0.1459	-0.0463	1.1093	18.5995	-33.7819	-2.0425
9	8.5149	-6.5324	-0.6127	5.0857	1.0968	5.3413	-0.1275	-0.3543	-1.1977	0.034	-0.2271	1.4324	0.1553	-0.5162	0.3805	0.2704	-0.0449	-0.1042	0.3448	0.0093	0.414	4.7582	-20.0913	9.2244
10	2.3719	-2.2232	-0.7862	3.6333	0.4446	1.1802	0.1519	-0.255	0.8982	0.049	0.0458	-1.2726	-0.2012	0.0525	0.0699	0.2776	-0.113	0.0327	0.1057	0.0597	0.3918	21.0043	3.9118	2.9131
11	3.3593	-1.4448	1.5877	7.2384	-5.2106	7.1181	0.0358	0.6062	0.6289	-0.6272	0.2464	0.2685	-0.3621	-0.1595	-0.5208	0.5935	-0.1347	0.2416	0.5458	0.3092	1.0226	21.7824	2.3373	-16.3461
12	0.453	-0.3204	0.0204	1.9024	-0.9884	1.9659	-0.1285	0.3464	0.1575	-0.2071	0.0395	-0.0703	-0.1966	-0.092	-0.2091	0.471	0.0141	0.1346	0.5825	0.2057	0.1728	19.0974	2.0735	-12.3851
13	2.2224	2.02	0.0994	2.0837	-0.2126	2.0871	0.734	1.7735	-1.7124	-1.6726	-0.069	0.5404	1.1918	-0.3525	-0.6657	1.0555	-0.138	-0.0026	0.7732	-0.1907	0.6393	13.3149	-16.5641	-13.248
14	2.7944	0.1983	-0.2016	0.1628	0.6932	3.3686	-0.1968	0.405	0.3506	-0.4338	0.0054	-0.4141	-0.3633	0.3941	-0.0201	0.3549	-0.0296	0.1886	0.3762	0.2511	0.5026	20.1813	2.475	-11.6347
15	1.2551	-0.5795	0.4053	2.7462	-0.0096	1.5469	-0.1057	0.133	0.3956	-0.1729	-0.1157	-1.1372	0.1107	0.3756	0.206	0.3304	0.0575	-0.0523	0.2387	0.0254	1.2934	32.9522	-6.5005	-1.8835
16	8.8053	2.0674	-6.026	2.4539	-0.7885	6.7043	-0.1592	-1.2705	0.7474	0.7037	0.1714	-0.8072	-0.2076	0.6756	-0.0102	0.3813	0.0505	-0.3092	0.3395	-0.0963	0.7966	22.216	3.6434	13.2501
17	3.0485	2.0233	-0.3873	3.8766	1.7154	1.5872	0.0317	0.162	0.7708	-0.0382	0.0326	-0.1366	-0.106	-0.1592	0.0259	0.2308	-0.0056	-0.0805	-0.0043	0.0915	0.4885	9.5276	2.6112	-3.6146
18	3.6994	-2.2671	1.3456	4.08	2.8733	5.57	-0.046	0.9948	-0.3866	-1.0175	-0.0947	-0.3151	0.7702	0.1062	0.1624	0.5159	-0.0539	0.0174	0.3262	0.0219	0.3306	4.1493	-9.8191	-6.6719
19	4.8135	-0.5501	0.8541	5.9867	2.908	4.4883	0.0877	-0.3684	0.9985	-0.0199	-0.1998	-0.1051	-0.2706	0.04	0.1243	0.2111	-0.028	0.0991	0.2998	-0.0913	0.3483	7.507	2.9848	4.8404
20	7.0481	0.9393	-0.2326	0.1826	-0.3696	2.0042	0.3495	-0.169	1.9483	-0.4522	-0.0178	0.2812	-1.0776	-0.0427	-0.3231	0.8971	-0.0366	-0.1475	0.3148	-0.1626	1.1353	-1.9312	16.3328	9.5505
21	4.6612	-2.5287	3.1938	1.9723	-3.052	5.3066	-0.7496	-1.0325	1.2735	0.6302	-0.1718	-0.3203	-1.3331	-0.655	1.079	1.0125	0.106	-0.7501	1.1335	-0.1999	1.4437	42.1107	-11.0534	24.4685
22	2.699	-0.3464	2.6522	1.398	0.002	2.8362	0.0075	-0.08	-0.234	0.1067	0.0843	-0.4054	0.09	0.5803	-0.1788	0.2557	-0.0087	-0.3243	0.42	0.0309	1.034	27.8499	-17.3995	12.9199
23	2.6057	2.7305	-0.1898	2.8661	-0.2738	1.2083	0.0069	-0.1223	0.0767	-0.0409	0.1936	-0.2431	-0.057	0.2071	-0.1542	0.1741	-0.0466	-0.0429	0.4317	0.0104	0.7359	13.9455	-11.9081	8.4918
24	6.7318	6.8822	-0.0984	7.6496	-0.0771	0.0024	0.1019	-0.1967	0.4474	0.4347	0.0121	-0.1547	-0.0103	0.0192	-0.0804	0.3405	0.0576	-0.1793	0.2544	-0.0624	0.6809	12.6504	-10.9084	3.604
25	3.5833	1.5125	-3.7124	1.6258	-2.224	4.5738	-0.198	0.5359	-0.8225	-0.4159	-0.0478	-0.4835	0.7634	0.01	0.2349	1.4756	0.2669	-0.4126	1.6063	0.0513	1.4085	2.0845	-22.6263	-3.9665
26	2.4685	0.55	-0.9205	3.8038	-4.3754	5.2919	0.152	1.637	-1.707	-1.2348	0.1117	1.8593	1.2476	-2.4062	-0.2551	0.4649	-0.0867	-0.2107	0.8038	-0.1252	0.9253	9.4855	-24.9207	-0.6044
27	1.0503	1.0966	0.6439	2.7464	0.0132	0.6645	-0.0984	-0.0482	0.0156	-0.0221	-0.0258	-0.3687	-0.0414	0.0415	0.0411	0.2377	0.0213	-0.1833	0.2198	-0.0418	0.9555	20.8009	-13.0758	3.6594
28	7.2706	-2.1041	0.0856	6.2182	-1.6697	7.0371	0.0898	-0.6612	-0.8231	0.3395	0.0733	0.1198	0.5331	0.241	-0.168	0.5735	-0.0255	-0.4231	0.42	0.0484	1.0383	27.6308	-14.8661	18.8802
29	3.9669	0.2362	5.0296	3.7738	2.5541	7.7267	0.1021	0.8695	-0.6859	0.1198	0.1056	-0.3697	0.1089	0.7925	-0.4183	0.6143	0.009	-0.5733	1.0872	0.0145	1.4121	44.3898	-19.2379	20.1863

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 102:118)
2	X-RAY DIFFRACTION	2	(chain A and resid 119:123)
3	X-RAY DIFFRACTION	3	(chain A and resid 124:133)
4	X-RAY DIFFRACTION	4	(chain A and resid 134:148)
5	X-RAY DIFFRACTION	5	(chain A and resid 149:161)
6	X-RAY DIFFRACTION	6	(chain A and resid 162:169)
7	X-RAY DIFFRACTION	7	(chain A and resid 170:175)
8	X-RAY DIFFRACTION	8	(chain A and resid 176:195)
9	X-RAY DIFFRACTION	9	(chain A and resid 196:210)
10	X-RAY DIFFRACTION	10	(chain A and resid 211:260)
11	X-RAY DIFFRACTION	11	(chain A and resid 261:272)
12	X-RAY DIFFRACTION	12	(chain A and resid 273:286)
13	X-RAY DIFFRACTION	13	(chain A and resid 287:292)
14	X-RAY DIFFRACTION	14	(chain A and resid 293:313)
15	X-RAY DIFFRACTION	15	(chain A and resid 314:343)
16	X-RAY DIFFRACTION	16	(chain A and resid 344:361)
17	X-RAY DIFFRACTION	17	(chain A and resid 362:394)
18	X-RAY DIFFRACTION	18	(chain A and resid 395:400)
19	X-RAY DIFFRACTION	19	(chain A and resid 401:414)
20	X-RAY DIFFRACTION	20	(chain A and resid 415:421)
21	X-RAY DIFFRACTION	21	(chain C and resid 1:4)
22	X-RAY DIFFRACTION	22	(chain C and resid 5:11)
23	X-RAY DIFFRACTION	23	(chain C and resid 12:12)
24	X-RAY DIFFRACTION	24	(chain C and resid 13:13)
25	X-RAY DIFFRACTION	25	(chain C and resid 17:17)
26	X-RAY DIFFRACTION	26	(chain C and resid 18:20)
27	X-RAY DIFFRACTION	27	(chain C and resid 21:24)
28	X-RAY DIFFRACTION	28	(chain C and resid 25:28)
29	X-RAY DIFFRACTION	29	(chain C and resid 29:32)

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