PDB-4e10: Protelomerase tela Y201A covalently complexed with substrate DNA

ID or keywords:

Entry

Database: PDB / ID: 40000000000

Title

Protelomerase tela Y201A covalently complexed with substrate DNA

Components

DNA (5'-D(*CP*AP*TP*AP*AP*(BRU)P*AP*AP*CP*AP*AP*(BRU)P*AP*T)-3')
DNA (5'-D(*CP*AP*TP*GP*AP*TP*AP*(BRU)P*(BRU)P*GP*(BRU)P*(BRU)P*AP*(BRU)P*(BRU)P*AP*(BRU)P*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: 2.506 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	4e10.cif.gz	181.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4e10.ent.gz	150.2 KB	Display	PDB format
PDBx/mmJSON format	4e10.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/e1/4e10 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e10	HTTPS FTP

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Related structure data

Related structure data	4dwpC 4e0gC 4e0jC 4e0pC 4e0yC 4e0zC C: citing same article (ref.)
Similar structure data	4e0y-1 1xd2-d 7kfz-d 4e0g-1 6d59-d 6cur-d 6d5w-d 4nym-d 6v9n-d 6bvi-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)
#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
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#172 - Apr 2014
RecA and Rad51
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#122 - Feb 2010
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#227 - Nov 2018
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similarity (1)
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#150 - Jun 2012
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#180 - Dec 2014
TAL Effectors
similarity (1)
#135 - Mar 2011
Integrase
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#155 - Nov 2012
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#87 - Mar 2007
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#73 - Jan 2006
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#139 - Jul 2011
DNA Methyltransferase
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Nucleosome
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#55 - Jul 2004
DNA Ligase
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#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
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#23 - Nov 2001
DNA
similarity (1)
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Two-component Systems
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#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Protelomerase

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

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

hetero molecules

63 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*(BRU)P*AP*AP*CP*AP*AP*(BRU)P*AP*T)-3')

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

hetero molecules

A: Protelomerase

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

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

hetero molecules

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

Unit cell

Length a, b, c (Å)	116.340, 119.660, 56.630
Angle α, β, γ (deg.)	90.00, 111.30, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Protelomerase / Telomere resolvase Mass: 52556.074 Da / Num. of mol.: 1 / Mutation: Y201A 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
#2: DNA chain	DNA (5'-D(CPAPTPAPAP(BRU)PAPAPCPAPAP(BRU)PAPT)-3') Mass: 4146.249 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain	DNA (5'-D(CPAPTPGPAPTPAP(BRU)P(BRU)PGP(BRU)P(BRU)PAP(BRU)P(BRU)PAP(BRU)PG)-3') Mass: 5989.702 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: 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
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.92 Å³/Da / Density % sol: 57.85 %
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 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. all: 18263 / Num. obs: 18263 / % possible obs: 73.5 % / 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: 2.506→35.05 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 30.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2701	954	5.23 %
R_work	0.1832	-	-
obs	0.1877	18246	73.49 %
all	-	18246	-

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-	3.7923 Å²	-0 Å²	-0.22 Å²
2-	-	0.0479 Å²	0 Å²
3-	-	-	-3.8402 Å²

Refinement step

Cycle: LAST / Resolution: 2.506→35.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2514	570	17	177	3278

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	3225
X-RAY DIFFRACTION	f_angle_d	1.837	4479
X-RAY DIFFRACTION	f_dihedral_angle_d	21.961	1197
X-RAY DIFFRACTION	f_chiral_restr	0.098	492
X-RAY DIFFRACTION	f_plane_restr	0.007	476

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 (%)
2.506-2.638	0.3692	43	0.2959	760	X-RAY DIFFRACTION	23
2.638-2.8032	0.3863	80	0.3035	1510	X-RAY DIFFRACTION	45
2.8032-3.0196	0.3278	131	0.2777	2248	X-RAY DIFFRACTION	68
3.0196-3.3232	0.3188	155	0.2222	3031	X-RAY DIFFRACTION	90
3.3232-3.8036	0.3089	180	0.1896	3248	X-RAY DIFFRACTION	97
3.8036-4.7902	0.2071	185	0.1389	3237	X-RAY DIFFRACTION	97
4.7902-35.0538	0.2283	180	0.1449	3258	X-RAY DIFFRACTION	95

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	7.7139	-3.8893	0.2295	3.3998	1.0569	2.2412	0.3824	0.5052	0.1386	-0.2768	-0.3512	-0.6095	-0.1426	0.1908	-0.0725	0.3509	0.1518	0.2945	0.4281	0.0777	1.7401	29.2506	-34.7712	-3.0934
2	8.7557	3.017	2.2284	4.6093	5.1014	6.2738	-0.0846	0.4344	-0.9048	-0.0352	0.7921	-0.7184	0.409	1.2956	-0.8258	0.5274	0.0454	-0.0223	0.7241	-0.1173	2.0494	37.9482	-26.1013	4.1079
3	2.2632	-1.2148	0.3906	5.9228	1.8318	4.8687	0.0331	-0.1335	-0.896	0.4613	0.0647	-1.3238	0.1696	0.9451	-0.0421	0.397	0.1326	-0.2333	0.2293	0.201	1.3069	30.3741	-32.022	7.6074
4	1.9831	-2.5745	-0.3699	5.8797	0.1309	2.043	-0.336	0.1152	-1.0507	0.8215	-0.0352	0.4374	-0.1182	-0.0737	-0.3261	0.6487	0.1027	0.0166	0.3106	0.0541	1.396	16.5056	-40.9644	6.8052
5	4.8592	-3.7306	3.7573	5.9987	1.8489	2.0004	-0.5639	-0.5621	-2.753	1.3701	-0.0702	-0.5402	0.8315	0.4508	0.2159	0.7382	0.0367	0.05	0.4032	0.1768	0.8658	18.5999	-32.0836	14.5883
6	4.9932	-2.6832	-1.0615	3.8461	3.2183	3.6855	0.2149	-0.0961	-1.2627	0.2511	-0.2205	-0.33	0.3052	-0.2376	0.1033	0.4337	0.0345	-0.0458	0.2354	0.0891	0.8644	17.8137	-29.8111	3.5529
7	5.3111	2.5139	2.6207	2.48	0.3063	3.4149	-1.1518	-0.8767	-1.6974	0.3351	0.96	0.6745	-0.3279	-0.6717	0.0886	0.82	0.0838	-0.0834	0.3633	0.1688	0.8353	3.8405	-22.0749	10.2967
8	7.0659	-5.4514	6.7975	4.8325	-5.2771	6.5407	0.1551	-0.5049	-0.8131	0.0561	1.1727	0.0452	0.6059	-1.0532	-0.7006	0.8057	0.0137	-0.133	0.4767	-0.0672	0.3411	3.624	-12.9897	10.6026
9	3.7345	1.0208	-0.6223	3.8774	0.2859	0.6423	0.0223	-0.1634	1.0625	-0.0884	0.0609	-0.886	-0.1193	0.1671	-0.0523	0.4275	-0.0282	-0.011	0.2887	-0.0278	0.8361	21.1583	3.164	0.9901
10	7.294	0.6789	1.6259	1.9143	0.0401	6.7099	-0.3401	1.4133	0.4998	-0.803	-0.0075	-0.1406	-1.1946	0.8809	0.0361	1.3865	-0.029	0.3215	1.0135	0.2453	0.5378	17.3488	11.588	-20.4611
11	5.3503	-1.1762	2.3916	3.1045	-3.2038	5.1189	-0.0162	0.9841	0.8609	0.0076	-0.0925	-1.2004	-0.7038	0.5748	-0.0299	0.5562	-0.012	0.1985	0.4494	-0.0098	0.4212	19.0636	-1.0827	-10.8256
12	2.004	-2.3909	9.7538	8.2873	-4.3648	1.998	0.7114	1.3961	-1.559	-0.6412	0.0122	-0.542	1.8915	-0.3052	-0.3138	0.8174	-0.0146	0.3097	0.872	-0.2051	0.7069	14.1173	-14.4412	-13.5859
13	1.5221	3.4145	3.2598	2.0029	6.3662	7.2607	-0.1262	0.6166	1.2882	-0.9466	0.8044	-0.469	-0.4436	0.3206	-0.3265	0.404	-0.0086	0.2692	0.4155	0.1025	0.8377	17.9717	3.3294	-11.6355
14	4.0387	-0.6106	0.789	1.2043	0.3654	0.4493	0.0233	0.2324	-0.4383	-0.2373	0.417	-1.2645	0.1426	-0.1662	0.89	0.3823	-0.1204	0.4291	0.4576	0.1813	1.7083	32.3895	3.6064	-8.9957
15	2.2124	-0.9789	-1.9259	4.6825	1.3025	7.6937	-0.3209	-0.0904	-0.2556	0.2012	0.2805	-1.598	0.5572	0.5358	0.088	0.4644	0.0374	-0.0395	0.2849	-0.1092	1.0322	32.0056	-9.4662	1.3004
16	4.5852	-5.7514	-6.0592	9.1391	7.2341	8.0755	-0.2884	-1.6601	1.421	1.125	0.3235	-0.895	0.101	0.5168	-0.0768	0.5817	0.0101	-0.2096	0.4832	-0.2257	0.6682	24.6622	4.7309	12.6784
17	7.3073	-3.7331	-0.8793	4.3086	3.169	3.1853	0.1944	-2.1531	0.9901	1.45	0.4636	-1.1651	0.2059	-0.3145	-0.6347	0.6923	-0.1347	-0.0545	0.532	-0.0078	0.4684	15.1654	2.804	16.3321
18	4.1143	0.66	2.0709	4.1279	0.5759	4.1396	-0.2961	0.4292	1.0319	-0.0411	0.2158	0.1187	-0.252	0.3133	-0.0028	0.3603	0.0394	0.1148	0.1755	0.0258	0.4391	10.2326	2.4748	-2.7435
19	7.4771	-0.2337	3.165	4.694	-1.1156	2.1753	-0.0293	0.4613	-1.0466	1.1158	0.7478	0.0286	0.7936	0.2042	0.2908	0.7388	-0.0091	0.0361	0.2793	-0.0834	0.3135	4.6402	-9.8876	-7.4354
20	0.865	0.6135	0.1206	0.6617	-0.9714	4.531	0.1194	-0.6078	0.8434	-0.187	0.5485	0.353	-0.9427	-0.4258	-0.0666	0.3812	-0.0029	-0.1161	0.2603	-0.2985	1.1815	4.8066	7.0861	6.0794
21	0.5602	-0.1209	1.5427	0.2042	-0.0821	4.5359	-0.4565	-0.7343	1.0182	0.1767	-0.0247	-0.1543	-0.7057	-0.5175	1.2099	1.1139	0.0328	-0.965	1.3192	-0.1156	1.9976	42.1281	-11.1476	24.3735
22	2.2278	0.2822	1.1733	0.057	0.2127	0.9737	-0.3262	0.0035	0.7464	0.8461	-0.091	-1.1668	-0.3751	0.6013	0.2795	0.5791	-0.0022	-0.3406	0.5234	0.0628	1.4224	30.2567	-17.5897	13.0561
23	4.0892	0.7583	-3.6538	8.2151	-0.3303	3.2717	-0.0477	-0.0211	0.4351	-0.1932	0.5113	0.2315	0.3887	-0.4017	-0.516	0.459	-0.0094	-0.1115	0.3779	0.0612	0.8678	13.4235	-13.2707	6.5269
24	0.9637	-1.4346	-1.8634	4.3187	3.869	4.1614	-0.0142	0.4716	-0.1472	-0.8374	-0.6948	1.485	-0.1049	-1.0074	0.5175	0.5713	0.0979	-0.1722	0.4243	-0.0851	0.9856	13.328	-22.4118	-0.5726
25	1.3228	0.1614	-1.9613	4.8617	-5.669	9.0202	-0.126	-0.5554	0.1043	0.5749	-0.0768	-0.9735	0.2881	0.6807	0.2882	0.6029	0.064	-0.3053	0.4704	-0.0543	1.1211	25.4886	-13.3119	12.5153
26	7.3673	-0.4754	1.6736	2.3968	2.9564	4.3561	-0.402	-1.1106	-0.5428	0.2883	-0.2491	-0.749	-0.7554	0.8863	-0.0584	1.0942	0.0091	-0.7982	1.2289	0.0533	1.9609	44.3234	-19.2061	20.4204

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 104:113)
2	X-RAY DIFFRACTION	2	(chain A and resid 114:120)
3	X-RAY DIFFRACTION	3	(chain A and resid 121:145)
4	X-RAY DIFFRACTION	4	(chain A and resid 146:157)
5	X-RAY DIFFRACTION	5	(chain A and resid 158:161)
6	X-RAY DIFFRACTION	6	(chain A and resid 162:197)
7	X-RAY DIFFRACTION	7	(chain A and resid 198:206)
8	X-RAY DIFFRACTION	8	(chain A and resid 207:210)
9	X-RAY DIFFRACTION	9	(chain A and resid 211:268)
10	X-RAY DIFFRACTION	10	(chain A and resid 269:276)
11	X-RAY DIFFRACTION	11	(chain A and resid 277:286)
12	X-RAY DIFFRACTION	12	(chain A and resid 287:295)
13	X-RAY DIFFRACTION	13	(chain A and resid 296:306)
14	X-RAY DIFFRACTION	14	(chain A and resid 307:323)
15	X-RAY DIFFRACTION	15	(chain A and resid 324:343)
16	X-RAY DIFFRACTION	16	(chain A and resid 344:355)
17	X-RAY DIFFRACTION	17	(chain A and resid 356:359)
18	X-RAY DIFFRACTION	18	(chain A and resid 360:394)
19	X-RAY DIFFRACTION	19	(chain A and resid 395:400)
20	X-RAY DIFFRACTION	20	(chain A and resid 401:421)
21	X-RAY DIFFRACTION	21	(chain C and resid 1:4)
22	X-RAY DIFFRACTION	22	(chain C and resid 5:10)
23	X-RAY DIFFRACTION	23	(chain C and resid 11:101)
24	X-RAY DIFFRACTION	24	(chain D and resid 18:21)
25	X-RAY DIFFRACTION	25	(chain D and resid 22:28)
26	X-RAY DIFFRACTION	26	(chain D and resid 29:32)

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