PDB-4e0p: Protelomerase tela covalently complexed with substrate DNA

ID or keywords:

Entry

Database: PDB / ID: 4e0p

Title

Protelomerase tela covalently complexed with 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*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')
Protelomerase

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: 2.2 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	4e0p.cif.gz	188.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4e0p.ent.gz	154.1 KB	Display	PDB format
PDBx/mmJSON format	4e0p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4e0p_validation.pdf.gz	853.4 KB	Display	wwPDB validaton report
Full document	4e0p_full_validation.pdf.gz	861.3 KB	Display
Data in XML	4e0p_validation.xml.gz	21 KB	Display
Data in CIF	4e0p_validation.cif.gz	31.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e0/4e0p ftp://data.pdbj.org/pub/pdb/validation_reports/e0/4e0p	HTTPS FTP

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Related structure data

Related structure data	4dwpC 4e0gC 4e0jC 4e0yC 4e0zC 4e10C C: citing same article (ref.)
Similar structure data	4e0j-1 4e0z-1 4azi-d 5yjw-1 4do4-d 6d56-d 6v94-d 4do6-d 4e0y-1 4e0g-1 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
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Thymine Dimers
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Cisplatin and DNA
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RecA and Rad51
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#180 - Dec 2014
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similarity (1)
#135 - Mar 2011
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DNA Ligase
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Estrogen Receptor
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similarity (1)
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lac Repressor
similarity (1)
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similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
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similarity (1)
#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*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')

hetero molecules

62.9 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*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*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)	117.583, 119.693, 62.944
Angle α, β, γ (deg.)	90.00, 113.94, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-673- HOH
2	1	D-224- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Protelomerase 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(CPAPTPGPAPTPAPTPTPGPTPTPAPTPTPAPTPG)-3') Mass: 5535.611 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 440 molecules

#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-DT / THYMIDINE-5'-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 Mass: 18.015 Da / Num. of mol.: 436 / 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: 3.24 Å³/Da / Density % sol: 62.06 %
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: 14-BM-C / Wavelength: 0.9 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2009
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 1.94→50 Å / Num. all: 3 / Num. obs: 58879 / % possible obs: 83.2 % / 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: 2.2→39.983 Å / SU ML: 0.3 / σ(F): 1.33 / Phase error: 31.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2492	1619	5.05 %
R_work	0.2012	-	-
obs	0.2037	32038	79.37 %
all	-	32047	-

Solvent computation

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

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.6852 Å²	0 Å²	-1.0303 Å²
2-	-	2.4322 Å²	0 Å²
3-	-	-	-12.312 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→39.983 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2528	593	29	436	3586

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3286
X-RAY DIFFRACTION	f_angle_d	1.467	4562
X-RAY DIFFRACTION	f_dihedral_angle_d	20.969	1263
X-RAY DIFFRACTION	f_chiral_restr	0.088	499
X-RAY DIFFRACTION	f_plane_restr	0.006	482

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 (%)
2.2002-2.2649	0.3792	70	0.2214	1500	X-RAY DIFFRACTION	47
2.2649-2.338	0.3084	80	0.2261	1642	X-RAY DIFFRACTION	51
2.338-2.4216	0.2563	100	0.243	1823	X-RAY DIFFRACTION	57
2.4216-2.5185	0.299	104	0.2538	2044	X-RAY DIFFRACTION	64
2.5185-2.6331	0.3083	133	0.2702	2254	X-RAY DIFFRACTION	71
2.6331-2.7719	0.3347	117	0.2638	2495	X-RAY DIFFRACTION	79
2.7719-2.9455	0.3211	151	0.2669	2812	X-RAY DIFFRACTION	88
2.9455-3.1729	0.3075	165	0.256	3107	X-RAY DIFFRACTION	97
3.1729-3.492	0.2393	185	0.1938	3150	X-RAY DIFFRACTION	99
3.492-3.9969	0.2414	163	0.1681	3182	X-RAY DIFFRACTION	99
3.9969-5.0341	0.1837	178	0.1517	3168	X-RAY DIFFRACTION	99
5.0341-39.9894	0.1989	173	0.1647	3242	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	0.2614	-0.2711	-0.1232	0.684	-0.3097	0.5333	0.0589	0.3047	-0.9774	-0.4904	-0.6089	1.6537	0.1818	-0.5965	0.5491	0.5157	0.076	0.1122	0.5039	-0.2195	1.6645	26.212	-37.7691	-5.8623
2	4.3767	-0.5336	5.079	1.8461	-0.9465	5.9535	-0.2423	0.0844	1.541	0.0055	-0.0777	-0.5485	-0.4279	0.2248	0.3197	0.3587	0.006	0.0144	0.493	0.1846	1.5689	35.8889	-25.6965	2.5256
3	9.5574	2.2275	-3.3071	3.7469	1.2632	6.0087	0.2849	-0.0984	0.2875	0.3526	0.1544	-2.0897	0.151	0.9415	-0.4299	0.7354	0.032	-0.4836	0.979	0.1728	1.882	40.4155	-21.5948	12.2112
4	0.9985	-0.2587	1.1099	1.0198	-0.097	2.7281	-0.2167	-0.0772	0.1859	0.4528	0.0885	-0.4124	0.08	0.3403	0.0576	0.3514	0.044	-0.1915	0.3368	0.1858	1.0383	29.1152	-31.2825	8.6777
5	0.75	-1.0164	0.131	4.9236	-0.7843	1.2752	-0.0649	0.0055	-0.4124	-0.2257	-0.067	0.4742	0.2033	-0.0867	0.1038	0.4145	0.0494	0.0819	0.2393	0.0772	1.2179	19.5861	-43.2062	2.5118
6	1.9314	-3.649	-1.2331	7.3411	2.3948	0.7965	-0.7246	-0.2593	0.1843	1.8317	0.3642	-0.5153	0.1169	0.4719	0.3253	0.6727	0.0505	-0.1498	0.4169	0.2882	0.9972	17.4908	-30.8097	13.7263
7	3.1037	-2.9946	0.0346	5.1629	2.4439	7.3547	0.0186	-0.1475	-0.0022	0.316	0.2242	-1.1944	-0.0237	0.5571	-0.1852	0.2005	-0.0155	-0.0673	0.1877	0.1224	0.487	19.1989	-25.6525	5.5267
8	2.1335	-2.3111	-0.3306	4.1681	-0.1774	1.9943	0.4022	0.2818	-0.0371	-0.5563	-0.3234	0.0313	-0.1371	-0.1149	-0.0501	0.354	0.086	0.041	0.2787	-0.0622	1.0865	18.1875	-34.0418	-3.5006
9	5.9	-3.3419	2.5203	2.7588	0.8482	9.3492	-0.4444	-0.8567	-1.0213	1.4323	0.3579	0.9431	0.4513	-0.7626	0.0725	0.3797	-0.0302	0.0272	0.3258	0.132	0.2991	5.237	-22.9946	8.7414
10	1.8301	-0.5679	-0.7169	3.2249	-0.6986	1.2204	0.1039	-0.3612	0.6108	0.3614	-0.0433	-0.6802	-0.2576	0.071	-0.1282	0.3151	-0.0004	-0.0275	0.2505	-0.1649	0.2479	12.4253	3.9088	8.1469
11	1.275	0.6968	-0.2909	1.8261	-0.8274	1.2932	-0.0262	0.0288	0.1766	-0.0878	0.0369	-0.5396	-0.1297	0.2241	0.0291	0.1931	-0.0626	0.2385	0.1457	0.0774	0.8587	27.2027	0.8168	-3.0179
12	2.5745	0.6706	-1.7189	1.0104	0.9158	4.4967	-0.0621	0.4797	0.57	-0.6541	0.5696	0.5321	-0.8758	-0.4301	-0.5706	0.7649	-0.0222	0.2723	0.6145	0.4243	1	18.4471	11.0528	-17.9327
13	1.7307	0.5546	-1.2507	1.5397	-1.3089	3.7443	-0.1982	0.3773	-0.1054	-0.3143	0.1895	-0.0888	0.4111	-0.3422	0.1589	0.4738	0.0642	0.2509	0.4537	0.073	0.1729	16.9289	-9.2245	-12.5357
14	1.2769	0.1292	-0.1018	0.0293	0.156	1.6318	-0.2149	0.2078	0.2909	-0.4584	0.2263	0.0525	-0.434	0.2305	-0.0019	0.3674	-0.0674	0.2333	0.3115	0.3088	0.7154	21.1895	7.4756	-10.7311
15	0.0278	0.1654	-0.0093	0.9781	-0.0505	0.0028	0.2143	0.2818	0.6182	-0.1898	-0.0886	-0.5144	-0.153	0.1338	-0.0823	0.3329	0.0635	0.211	0.3503	0.0888	1.3057	34.6257	-3.0655	-6.22
16	4.4567	-5.423	4.5219	6.69	-5.6843	4.9515	-0.1303	0.3595	0.6429	0.2414	-0.0323	-2.2398	0.2143	1.0462	0.1635	0.3781	0.0606	-0.0434	0.3518	-0.0145	1.1624	31.7453	-12.3645	2.5048
17	1.6775	1.4057	-0.0936	3.2942	1.242	1.4968	0.1154	-0.7528	0.402	0.1994	-0.1916	0.1394	-0.2177	-0.0031	0.1223	0.3053	-0.031	-0.2856	0.3699	-0.1992	0.692	23.827	1.801	12.2872
18	2.309	0.3567	0.9649	2.4932	0.1077	2.1336	-0.0479	0.4007	0.63	-0.2493	0.0679	-0.2828	-0.2378	-0.0369	-0.0251	0.2464	0.0229	0.1388	0.1793	0.1062	0.287	9.3158	3.013	-3.8009
19	4.1279	0.4423	0.3667	3.8232	-0.2921	3.8284	0.0354	-0.0869	0.1596	0.0267	0.0351	0.0333	-0.1671	-0.0728	-0.0197	0.2118	0.0247	-0.0036	0.1503	-0.1413	0.104	7.0194	-0.9909	1.1568
20	9.3814	2.0851	3.8903	5.8843	-1.8331	4.854	-0.2058	-1.0793	1.4673	0.9438	-0.0575	0.5371	-1.4892	-1.0295	0.2904	0.8149	0.0807	0.06	0.6737	-0.3991	0.8633	0.1334	15.6468	8.9694
21	4.1791	0.4783	5.1857	4.779	0.746	9.7421	-0.6196	-1.1862	1.5273	1.1451	-0.6024	-0.6455	-1.5725	-0.1542	1.29	1.1607	-0.0625	-0.864	1.9581	-0.1764	1.6678	40.6427	-10.5148	24.7666
22	2.5971	-1.9626	2.0589	2.2054	-0.351	4.6243	-0.1185	-0.3703	0.1449	0.206	0.0744	-0.5139	-0.0485	0.5654	0.0429	0.4219	-0.0224	-0.3846	0.5071	0.101	0.7186	27.8224	-16.8564	13.151
23	0.3772	-1.0169	0.9055	3.2823	-2.9657	2.6824	0.0214	-0.1627	-0.096	0.1274	0.0861	-0.0338	-0.0234	-0.324	-0.1097	0.2621	-0.0436	-0.0226	0.2355	0.1168	0.1608	13.418	-10.7964	6.0571
24	7.6175	-0.5786	-2.304	4.1896	-1.1443	1.1167	-0.0641	1.6012	-0.5054	-1.1564	-0.2506	1.3113	-0.2408	-1.2169	0.2486	0.3534	0.1489	-0.1208	0.6303	-0.1428	0.4738	7.8148	-23.5777	-1.4136
25	2.7471	3.42	1.2125	4.3186	1.9536	3.7229	-0.1752	-0.3548	0.04	0.1763	-0.0549	-0.5512	0.0587	0.2797	0.1492	0.2119	0.0562	-0.1335	0.17	-0.0188	0.4587	20.9313	-12.4028	3.8049
26	5.6826	-2.9284	1.1489	2.4547	-1.189	3.334	0.0061	-1.1155	-0.617	0.3654	0.356	-0.1426	0.5761	0.3258	-0.2416	0.6177	0.0396	-0.4542	0.7965	0.079	0.6699	27.5621	-14.3009	19.2007
27	3.3157	-3.2146	-1.8057	7.079	-0.6029	6.2592	0.0366	-0.647	-0.0491	0.4605	0.0588	-1.13	-0.2215	1.1279	-0.0771	0.6515	0.0497	-0.6463	1.5913	0.0198	1.2157	43.574	-17.9638	21.0276

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 102:110)
2	X-RAY DIFFRACTION	2	(chain A and resid 111:119)
3	X-RAY DIFFRACTION	3	(chain A and resid 120:126)
4	X-RAY DIFFRACTION	4	(chain A and resid 127:139)
5	X-RAY DIFFRACTION	5	(chain A and resid 140:153)
6	X-RAY DIFFRACTION	6	(chain A and resid 154:166)
7	X-RAY DIFFRACTION	7	(chain A and resid 167:180)
8	X-RAY DIFFRACTION	8	(chain A and resid 181:195)
9	X-RAY DIFFRACTION	9	(chain A and resid 196:206)
10	X-RAY DIFFRACTION	10	(chain A and resid 207:235)
11	X-RAY DIFFRACTION	11	(chain A and resid 236:265)
12	X-RAY DIFFRACTION	12	(chain A and resid 266:278)
13	X-RAY DIFFRACTION	13	(chain A and resid 279:297)
14	X-RAY DIFFRACTION	14	(chain A and resid 298:312)
15	X-RAY DIFFRACTION	15	(chain A and resid 313:331)
16	X-RAY DIFFRACTION	16	(chain A and resid 332:337)
17	X-RAY DIFFRACTION	17	(chain A and resid 338:362)
18	X-RAY DIFFRACTION	18	(chain A and resid 363:395)
19	X-RAY DIFFRACTION	19	(chain A and resid 396:412)
20	X-RAY DIFFRACTION	20	(chain A and resid 413:421)
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 12:16)
24	X-RAY DIFFRACTION	24	(chain D and resid 17:20)
25	X-RAY DIFFRACTION	25	(chain D and resid 21:24)
26	X-RAY DIFFRACTION	26	(chain D and resid 25:28)
27	X-RAY DIFFRACTION	27	(chain D and resid 29:32)

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