PDB-4gew: Crystal structure of TDP2 from C. elegans

ID or keywords:

Entry

Database: PDB / ID: 4gew

Title

Crystal structure of TDP2 from C. elegans

Components

5'-tyrosyl-DNA phosphodiesterase

Keywords

HYDROLASE / 5'-phosphotyrosyl-DNA diesterase

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 /

FOURIER SYNTHESIS / Resolution: 2.35 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	Aug 2, 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	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gew.cif.gz	149.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4gew.ent.gz	121 KB	Display	PDB format
PDBx/mmJSON format	4gew.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/ge/4gew ftp://data.pdbj.org/pub/pdb/validation_reports/ge/4gew	HTTPS FTP

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Related structure data

Related structure data	4f1hC 4f1iC 4fpvC 4fvaC C: citing same article (ref.)
Similar structure data	4f1i-1 4tn7-d 2h8c-d 2ant-d 4z13-d 6rxb-d 4dvf-d 4nqy-d 5lrw-d 2yk0-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

41.8 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
83.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.273, 101.273, 120.891
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-575- HOH

#1: Protein	5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase Mass: 40943.160 Da / Num. of mol.: 1 / Fragment: unp residues 1-362 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.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.79 Å³/Da / Density % sol: 67.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 15% polyethylene glycol (PEG) 6,000, 0.3M ammonium chloride, and 0.1M MES-NaOH, pH 6.0, 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: Aug 12, 2011
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: 2.35→50 Å / Num. all: 28157 / Num. obs: 28157 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHENIX		model building
PHENIX	(phenix.refine: dev_1114)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 2.35→46.19 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 20.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2072	1348	5.03 %	Random
R_work	0.1733	-	-	-
all	0.175	26806	-	-
obs	0.1733	26806	99.88 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.35→46.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2600	0	54	137	2791

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2704
X-RAY DIFFRACTION	f_angle_d	0.912	3627
X-RAY DIFFRACTION	f_dihedral_angle_d	13.997	995
X-RAY DIFFRACTION	f_chiral_restr	0.066	383
X-RAY DIFFRACTION	f_plane_restr	0.003	466

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 (%)
2.3499-2.4339	0.2602	138	0.2418	2476	X-RAY DIFFRACTION	99
2.4339-2.5313	0.2637	132	0.2221	2495	X-RAY DIFFRACTION	100
2.5313-2.6465	0.2563	125	0.2127	2499	X-RAY DIFFRACTION	100
2.6465-2.786	0.223	131	0.2025	2515	X-RAY DIFFRACTION	100
2.786-2.9606	0.2571	147	0.1888	2502	X-RAY DIFFRACTION	100
2.9606-3.1891	0.2396	128	0.1847	2540	X-RAY DIFFRACTION	100
3.1891-3.5099	0.1969	134	0.1619	2533	X-RAY DIFFRACTION	100
3.5099-4.0176	0.1862	140	0.1493	2557	X-RAY DIFFRACTION	100
4.0176-5.0607	0.1474	128	0.1442	2608	X-RAY DIFFRACTION	100
5.0607-46.1993	0.2239	145	0.1813	2733	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	8.1392	0.2003	0.851	4.2717	4.158	4.2577	-0.3869	0.306	0.462	-0.7401	0.2181	-0.6442	-1.2568	1.5126	0.0287	0.8315	-0.1412	-0.0863	0.6145	-0.1037	0.5496	31.4336	75.9312	76.0054
2	5.3757	3.627	5.4683	2.4332	3.6956	5.588	0.2871	1.4043	0.297	-0.482	-0.0757	-0.4051	-1.7652	1.0657	-0.0371	0.9945	0.0444	-0.0407	0.7788	-0.0881	0.5825	35.1943	75.4974	92.0293
3	3.4989	-4.1354	0.8976	5.8355	0.3739	2.3397	1.3778	1.6011	-1.0442	-0.2073	-1.033	0.0581	-0.3102	-0.3633	-0.7941	1.3634	-0.1526	-0.0247	1.3918	0.008	1.2984	46.429	77.429	86.0558
4	4.8829	4.3306	-4.1393	4.3281	-3.0921	6.8519	0.14	-1.3887	0.7308	0.5489	0.0728	-1.5044	-2.6343	2.1332	-0.1645	1.1435	-0.4197	0.0108	1.6999	-0.3075	0.9695	57.023	66.9263	84.6256
5	6.788	-1.9903	3.855	2.0267	-0.2836	9.62	-0.6554	-0.032	-1.1819	1.5638	0.1387	-0.9387	0.7153	0.1489	0.6099	1.0394	0.071	-0.0419	1.4286	-0.2651	1.0846	50.998	58.8644	86.0992
6	7.5124	3.6609	5.9732	2.9925	5.287	9.525	-0.676	1.0575	-0.0525	-1.0633	1.1538	-1.15	-1.1153	2.6967	-0.5672	0.7686	-0.1896	0.0521	1.3855	-0.2296	0.8962	54.0888	58.5251	75.5397
7	4.7735	-4.4357	-1.7577	4.0849	1.7758	1.2951	-0.4943	0.1039	0.6466	0.4892	0.5069	-0.3776	0.7774	0.0019	0.1545	0.7321	0.1956	-0.1159	0.8817	-0.2161	0.5711	44.6701	43.1343	78.7802
8	7.8998	-5.0537	-5.4263	3.5056	3.4693	3.726	0.1155	-1.3391	-0.4223	0.6782	0.7304	0.0258	0.1912	0.6586	-1.0453	0.6673	-0.0679	0.1017	0.6694	0.0617	0.5168	53.7936	21.0431	64.7942
9	6.9209	-2.0983	-3.3849	6.5859	2.616	8.0732	-0.0942	0.4034	-0.3636	-0.3904	0.0594	-0.0949	0.5092	0.0818	0.0515	0.4903	-0.0463	0.0394	0.3916	-0.0167	0.3785	57.322	14.114	44.0564
10	4.9229	0.4283	-1.5889	8.5044	-1.8009	6.1324	-0.1416	0.6176	-0.3802	-0.7251	0.136	0.414	0.8189	-0.5483	-0.0186	0.4145	-0.1009	-0.002	0.5213	-0.061	0.3637	47.8888	15.6048	43.62
11	4.4654	-5.0003	4.181	5.5608	-4.645	4.0129	-0.2867	-1.0752	0.0747	1.1164	0.2301	1.0985	-0.4779	-1.1116	0.1157	0.7242	-0.0143	0.0592	0.9304	0.0496	0.6313	40.3116	23.2679	53.9814
12	6.8983	3.7173	-5.1713	7.7321	-3.7793	7.5211	0.1472	0.8287	0.1791	-0.7674	0.1609	0.2459	-0.3061	-0.5568	-0.3856	0.4587	0.0384	0.0029	0.6759	0.0673	0.3872	48.9396	31.5102	39.4258
13	5.6433	1.5917	-3.9014	5.3391	-4.1336	9.739	0.3413	-0.1181	0.1541	0.3197	0.0357	0.4387	-0.5536	-0.817	-0.4451	0.2997	-0.0054	0.0211	0.4564	0.0231	0.3767	48.3647	27.8864	52.4544
14	8.0815	-5.6365	0.8401	5.2159	2.5934	8.6099	0.0744	0.5214	0.2414	-0.4393	-0.2457	-0.1149	-0.5906	0.2405	0.0838	0.607	0.0098	0.138	0.446	0.0743	0.4932	59.0157	38.208	40.7709
15	9.3846	-2.3797	-5.7201	5.9633	-0.239	5.5934	0.2552	0.0944	0.3129	0.4471	-0.1212	0.179	-0.5175	-0.3235	-0.1473	0.5201	0.0035	-0.0043	0.5103	-0.0388	0.4046	52.2785	34.7359	53.178
16	2.4954	-2.454	-3.1094	2.6216	2.5536	9.5927	0.6564	-0.1763	2.0442	-1.0477	0.2164	-0.6788	-1.151	1.0257	-1.3463	1.0941	-0.0657	0.0155	0.6797	-0.1657	0.6373	63.6127	41.5557	48.4506
17	8.8316	-4.8148	-3.4613	9.9116	0.2455	6.8067	0.2634	-0.7814	0.7628	0.967	-0.2433	-0.0544	-1.237	0.1943	-0.0903	0.6853	-0.04	0.091	0.5828	-0.0825	0.4374	60.1272	35.2976	58.2314
18	8.6466	-1.7792	-4.5693	8.7626	6.0464	8.8846	0.0387	-0.6765	0.1748	0.1093	0.2454	-0.3252	0.0407	1.163	-0.3291	0.3925	-0.01	0.0227	0.4772	0.0295	0.3773	71.4487	23.5574	48.4816
19	8.7567	-1.9754	-5.2523	2.9112	0.8569	7.0898	0.3862	0.1857	0.1393	-0.3185	-0.2206	-0.3228	0.0159	0.3492	-0.0173	0.4107	0.0215	0.0316	0.354	0.0351	0.3133	66.3273	28.18	47.5606
20	7.2276	-5.3158	-5.4454	6.8705	5.12	4.2877	-0.241	-0.4204	-0.1384	0.353	0.2246	-0.0988	0.8706	0.4815	0.0083	0.5396	-0.0102	0.0238	0.4916	0.0281	0.3734	64.4736	17.1574	52.1552

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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