PDB-4f1i: Crystal structure of SeMet TDP2 from Caenorhabditis elegans

ID or keywords:

Entry

Database: PDB / ID: 4f1i

Title

Crystal structure of SeMet TDP2 from Caenorhabditis elegans

Components

5'-tyrosyl-DNA phosphodiesterase

Keywords

HYDROLASE / 5'-tyrosyl DNA phosphodiesterase

Function / homology

Function and homology information

5'-tyrosyl-DNA phosphodiesterase activity /

nuclease activity /

Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / PML body / double-strand break repair /

single-stranded DNA binding / identical protein binding /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Shi, K. / Kurahashi, K. / Aihara, H.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Authors: Shi, K. / Kurahashi, K. / Gao, R. / Tsutakawa, S.E. / Tainer, J.A. / Pommier, Y. / Aihara, H.

History

Deposition	May 7, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 2, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4f1i.cif.gz	148.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4f1i.ent.gz	125.9 KB	Display	PDB format
PDBx/mmJSON format	4f1i.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/f1/4f1i ftp://data.pdbj.org/pub/pdb/validation_reports/f1/4f1i	HTTPS FTP

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Related structure data

Related structure data	4f1hC 4fpvC 4fvaC 4gewC C: citing same article (ref.)
Similar structure data	4gew-1 1nw2-6 5kms-1 5lrw-d 2r10-d 4tn7-d 6umr-d 4nwz-3 6rxb-d 4z13-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	#18 - Jun 2001 Myosin similarity (3) #19 - Jul 2001 Actin similarity (3) #60 - Dec 2004 Ubiquitin similarity (1) #81 - Sep 2006 Elongation Factors similarity (1)

Deposited unit

A: 5'-tyrosyl-DNA phosphodiesterase

hetero molecules

42.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 5'-tyrosyl-DNA phosphodiesterase

hetero molecules

A: 5'-tyrosyl-DNA phosphodiesterase

hetero molecules

defined by author&software
84.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	100.685, 100.685, 121.375
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase Mass: 41505.898 Da / Num. of mol.: 1 / Fragment: unp residues 21-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: Y63D3A.4 / Production host: Escherichia coli (E. coli) References: UniProt: Q9XWG3, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.94 Å³/Da / Density % sol: 68.76 %
Crystal grow	Temperature: 293 K / pH: 6 Details: PEG 6.000, 0.3M ammonium chloride, and 0.1M MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 96 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979
Detector	Type: NOIR-1 / Detector: CCD / Date: Sep 9, 2011
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: 2.5→50 Å / Num. obs: 23342 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / R_merge(I) obs: 0.126 / R_sym value: 0.126 / Net I/σ(I): 8.3
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.828 / Mean I/σ(I) obs: 2.1 / R_sym value: 0.828 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice	ice	data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.7.3_928)	refinement
d*TREK		data reduction
d*TREK		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→46.185 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 22.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2288	1134	5.11 %
R_work	0.1822	-	-
obs	0.1845	22208	99.95 %
all	-	22208	-

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-	2.9055 Å²	0 Å²	-0 Å²
2-	-	2.9055 Å²	-0 Å²
3-	-	-	-5.8111 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→46.185 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2626	0	48	142	2816

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2720
X-RAY DIFFRACTION	f_angle_d	0.878	3652
X-RAY DIFFRACTION	f_dihedral_angle_d	15.538	999
X-RAY DIFFRACTION	f_chiral_restr	0.074	389
X-RAY DIFFRACTION	f_plane_restr	0.002	469

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 (%)
2.5001-2.6139	0.3206	125	0.2543	2586	X-RAY DIFFRACTION	100
2.6139-2.7517	0.2833	168	0.2282	2559	X-RAY DIFFRACTION	100
2.7517-2.9241	0.2611	154	0.2061	2574	X-RAY DIFFRACTION	100
2.9241-3.1498	0.2811	157	0.2097	2579	X-RAY DIFFRACTION	100
3.1498-3.4667	0.2618	130	0.191	2644	X-RAY DIFFRACTION	100
3.4667-3.9681	0.2058	128	0.1641	2630	X-RAY DIFFRACTION	100
3.9681-4.9984	0.1656	128	0.1425	2677	X-RAY DIFFRACTION	100
4.9984-46.193	0.2363	144	0.1931	2825	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	2.4211	0.1844	-0.5642	2.2503	-6.9002	2.1396	-0.725	0.7781	0.2501	-0.5867	-0.4641	-0.8419	-1.1869	1.0302	1.258	0.6787	-0.1844	-0.088	0.5306	-0.0544	0.5287	31.2339	75.7892	76.4529
2	2.1267	2.0765	6.2776	1.9573	2.088	2.0562	-0.0926	0.6126	0.7296	0.2044	0.5224	-0.677	-1.221	0.2087	-0.3694	0.6731	0.1401	-0.0834	0.5171	-0.0553	0.6243	34.9322	75.1928	92.5234
3	6.9477	-0.7319	-2.8275	0.3452	-0.0094	1.4675	0.0642	1.8325	0.4876	0.5336	-0.5451	-0.9994	1.1793	-0.8244	-0.044	1.1828	-0.3535	-0.1142	0.9158	-0.0046	1.0844	46.2109	77.1931	86.6136
4	2.0609	5.6923	-2.5234	5.3593	0.1451	1.1692	0.4863	-1.3961	1.024	0.5893	-0.3289	-0.6626	-1.6228	0.9423	0.0118	0.8327	-0.3431	-0.0757	1.4622	-0.2194	1.0081	56.5934	66.7399	85.1138
5	2.0579	-4.018	0.1107	2.0279	5.4216	1.208	-0.1734	-0.3331	0.0776	1.911	-0.3917	-1.6377	0.9749	1.1276	0.3544	0.7737	0.1404	-0.1068	1.2433	-0.1841	0.9577	50.7674	58.6293	86.4667
6	2.7117	2.3709	5.4199	7.3052	5.5508	5.8598	-0.8264	1.458	-0.3808	-0.9109	1.7606	-1.907	-0.4396	2.7095	-0.8747	0.738	-0.1158	-0.0177	1.4052	-0.3147	0.8815	53.8582	58.3089	76.0165
7	0.3765	-1.0524	-0.8632	7.9565	4.6964	2.5018	-0.3189	-0.2258	0.0286	0.9003	-0.0376	0.2223	1.0946	-0.4619	0.4186	0.8109	0.1989	-0.0848	1.0036	-0.2501	0.5772	44.4531	38.4087	77.4859
8	2.8306	-1.0421	-7.0993	2.6068	-0.1918	2.2847	-0.0445	-0.5019	-0.4036	0.7052	-0.0872	-0.0472	0.7534	0.831	0.1724	0.4979	-0.0586	0.0043	0.4963	0.0405	0.4496	53.9063	20.7897	64.512
9	5.7434	-1.1196	-3.6172	6.7251	1.5314	6.9319	-0.0227	0.4352	-0.3556	-0.4218	-0.138	-0.2808	0.6635	-0.045	0.1725	0.3578	-0.0008	0.0055	0.283	-0.0318	0.2928	57.0926	13.8651	44.344
10	4.8948	0.311	-1.0393	6.3167	-0.7147	2.9218	-0.2344	0.7341	-0.3968	-0.7279	0.0137	0.2262	0.7835	-0.8625	0.2798	0.3729	-0.0673	0.027	0.4585	-0.0746	0.3548	47.6442	15.3998	44.0249
11	2.8668	-6.1337	2.3697	2.6422	-8.0521	2.4774	-0.4798	-1.0482	0.0104	1.1704	0.8173	0.3309	-0.9122	-1.3626	-0.7252	0.5748	-0.0115	0.0099	0.7855	-0.0729	0.6787	40.5355	22.8796	54.8256
12	7.4411	1.4666	-4.4394	8.9794	-3.5266	4.3692	-0.0811	0.9449	0.2514	-0.8768	0.2292	0.1508	0.1149	-0.2966	-0.1575	0.3686	0.0211	-0.0215	0.5539	0.0441	0.3041	48.9011	31.2773	39.5225
13	6.5963	2.4915	-7.1773	5.0441	-2.7349	2.9131	0.1503	0.0372	0.3196	-0.0002	0.1644	0.3819	-0.1054	-0.392	-0.3291	0.2087	0.0036	0.0005	0.4293	0.0275	0.2591	48.2281	27.7579	52.7362
14	3.1658	-8.1317	-1.6304	9.756	5.4285	6.9887	0.304	-0.1029	0.2347	-0.5346	-0.2617	-0.1179	-0.9286	0.4947	-0.048	0.4288	0.0015	0.0768	0.3632	0.065	0.4098	58.6911	37.9396	41.211
15	3.2912	-0.3014	-1.6908	3.7652	-1.0696	6.1731	0.358	0.0549	0.4076	0.5428	-0.2683	0.1555	-0.7218	-0.5275	-0.0894	0.3734	-0.0007	0.0296	0.2915	-0.0303	0.3283	52.113	34.6099	53.3863
16	2.1857	3.2019	-3.153	2.1461	0.3969	2.1688	2.138	0.3607	2.2215	-1.0016	-0.3718	-0.2733	-3.3604	-0.1212	-1.6073	0.9697	-0.1044	0.1814	0.6312	0.1058	0.601	63.265	41.1689	48.8979
17	2.3735	-6.336	-0.9778	9.3331	-1.6714	2.3453	0.0036	-0.9014	1.3609	1.0236	0.2064	-0.5325	-1.0999	0.5002	-0.3112	0.5427	-0.0474	0.0771	0.4894	-0.0592	0.5332	60.0557	35.1846	58.4235
18	6.0966	-1.8531	-4.5062	7.9401	4.3094	2.9657	-0.0346	-0.6089	0.2692	0.1451	0.1701	-0.3492	0.0377	1.0135	-0.3254	0.3437	-0.0364	0.0092	0.384	0.0084	0.3427	71.222	23.3314	48.6547
19	5.1819	-2.8219	-5.0991	4.032	1.864	7.6857	0.3857	0.518	0.0036	-0.2494	-0.4251	-0.3695	-0.2046	-0.4168	0.2896	0.3535	-0.0226	-0.0037	0.3661	0.0091	0.3392	66.1899	28.0899	47.6259
20	6.4369	-4.623	-5.4788	6.7545	5.4766	4.4253	-0.2361	-0.3828	-0.1816	0.2404	0.3193	-0.0526	0.7045	0.4539	-0.0178	0.3459	0.0117	0.0223	0.2949	0.0306	0.3097	64.3228	16.978	52.2645

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 21:27)
2	X-RAY DIFFRACTION	2	(chain A and resid 28:34)
3	X-RAY DIFFRACTION	3	(chain A and resid 35:41)
4	X-RAY DIFFRACTION	4	(chain A and resid 42:52)
5	X-RAY DIFFRACTION	5	(chain A and resid 53:61)
6	X-RAY DIFFRACTION	6	(chain A and resid 62:89)
7	X-RAY DIFFRACTION	7	(chain A and resid 90:114)
8	X-RAY DIFFRACTION	8	(chain A and resid 115:123)
9	X-RAY DIFFRACTION	9	(chain A and resid 124:161)
10	X-RAY DIFFRACTION	10	(chain A and resid 162:193)
11	X-RAY DIFFRACTION	11	(chain A and resid 194:201)
12	X-RAY DIFFRACTION	12	(chain A and resid 202:217)
13	X-RAY DIFFRACTION	13	(chain A and resid 218:235)
14	X-RAY DIFFRACTION	14	(chain A and resid 236:251)
15	X-RAY DIFFRACTION	15	(chain A and resid 252:276)
16	X-RAY DIFFRACTION	16	(chain A and resid 277:281)
17	X-RAY DIFFRACTION	17	(chain A and resid 282:290)
18	X-RAY DIFFRACTION	18	(chain A and resid 291:311)
19	X-RAY DIFFRACTION	19	(chain A and resid 312:329)
20	X-RAY DIFFRACTION	20	(chain A and resid 330:362)

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