PDB-4xhw: Crystal structure of Timeless_PAB domain in SeMet-labelled form

ID or keywords:

Entry

Database: PDB / ID: 4xhw

Title

Crystal structure of Timeless_PAB domain in SeMet-labelled form

Components

Protein timeless homolog

Keywords

REPLICATION / DNA damage response

Function / homology

Function and homology information

cellular response to bleomycin / detection of abiotic stimulus / replication fork arrest / cell cycle phase transition / cellular response to cisplatin / cellular response to hydroxyurea / DNA replication checkpoint signaling / replication fork protection complex / positive regulation of double-strand break repair / branching morphogenesis of an epithelial tube ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.85 Å

Authors

Xie, S. / Qian, C.

Funding support

Hong Kong, 2items

Citation

Journal: Mol.Cell / Year: 2015
Title: Timeless Interacts with PARP-1 to Promote Homologous Recombination Repair.
Authors: Xie, S. / Mortusewicz, O. / Ma, H.T. / Herr, P. / Poon, R.R. / Helleday, T. / Qian, C.

History

Deposition	Jan 6, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 30, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2015	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4xhw.cif.gz	153.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4xhw.ent.gz	129.9 KB	Display	PDB format
PDBx/mmJSON format	4xhw.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/xh/4xhw ftp://data.pdbj.org/pub/pdb/validation_reports/xh/4xhw	HTTPS FTP

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Related structure data

Related structure data	4xhtC 4xhuC C: citing same article (ref.)
Similar structure data	4xht-1 4xht-2 1t4e-d 4u88-d 3h8h-4 2qnd-1 4qwq-d 3hx1-d 1mvk-1 3uf4-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Protein timeless homolog

B: Protein timeless homolog

C: Protein timeless homolog

D: Protein timeless homolog

46.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein timeless homolog

B: Protein timeless homolog

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

2

C: Protein timeless homolog

D: Protein timeless homolog

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	66.597, 100.083, 149.581
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A and segid A
2	1	chain B and segid B
3	1	chain C and segid C
4	1	chain D and segid D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A
2	1	1	CHAIN B
3	1	1	CHAIN C
4	1	1	CHAIN D

#1: Protein	Protein timeless homolog / hTIM Mass: 11670.779 Da / Num. of mol.: 4 / Fragment: PAB domain (UNP RESIDUES 1000-1098) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TIMELESS, TIM, TIM1, TIMELESS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNS1

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.03 Å³/Da / Density % sol: 59.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 25% PEG 3350, 200mM sodium acetate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97923 Å / Relative weight: 1
Reflection	Resolution: 2.85→24.93 Å / Num. obs: 12777 / % possible obs: 100 % / Redundancy: 14.2 % / Net I/σ(I): 27.1

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Resolution: 2.85→24.93 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2534	573	4.78 %
R_work	0.1926	11425	-
obs	0.1954	11998	99.93 %

Solvent computation

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

Displacement parameters

B_iso max: 155.29 Å² / B_iso mean: 46.8777 Å² / B_iso min: 20 Å²

Refinement step

Cycle: final / Resolution: 2.85→24.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2854	0	0	0	2854
Num. residues	-	-	-	-	364

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2908
X-RAY DIFFRACTION	f_angle_d	1.397	3944
X-RAY DIFFRACTION	f_chiral_restr	0.058	437
X-RAY DIFFRACTION	f_plane_restr	0.007	531
X-RAY DIFFRACTION	f_dihedral_angle_d	16.475	1110

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1676	X-RAY DIFFRACTION	7.218	TORSIONAL
1	2	B	1676	X-RAY DIFFRACTION	7.218	TORSIONAL
1	3	C	1676	X-RAY DIFFRACTION	7.218	TORSIONAL
1	4	D	1676	X-RAY DIFFRACTION	7.218	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2.8501-3.1364	0.2897	141	0.2646	2801	2942
3.1364-3.5891	0.2909	151	0.2192	2817	2968
3.5891-4.5175	0.2437	147	0.1753	2830	2977
4.5175-24.9311	0.2239	134	0.1687	2977	3111

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	7.2828	-1.6494	0.3329	4.3938	0.9953	4.7594	0.1614	-0.5921	-1.049	-0.3616	0.1226	0.5269	-0.1239	0.0766	-0.0514	0.3578	0.0179	-0.0273	0.1543	0.0458	0.3469	11.1786	212.5006	145.1907
2	2.9633	-1.0017	1.2236	4.2715	-0.2763	1.8566	-0.2008	-0.222	0.7477	0.8563	-0.0854	-0.3426	-0.4441	-0.7113	-0.1608	0.6052	0.1762	-0.1085	0.4785	-0.029	0.0149	9.0206	218.622	155.4811
3	1.3168	1.7795	0.8704	7.3991	-2.7251	7.4226	-0.3716	-0.2432	-0.0866	-0.1572	0.067	-0.7249	-0.0308	1.0507	0.1056	0.3209	0.0174	0.0006	0.4107	-0.0852	0.4708	22.4566	216.503	150.1315
4	3.8081	-0.6905	3.0487	3.3805	1.7958	5.4462	-0.1813	0.8392	1.2946	-0.6882	-0.5751	-0.6161	-1.2436	0.7038	0.1891	0.6934	0.109	-0.1373	-0.2518	0.1694	0.4403	15.2792	225.4479	146.741
5	1.6697	0.9871	-0.0143	1.9282	0.2523	1.8106	0.2784	0.348	0.0775	-0.2067	-0.1947	0.1919	-0.1082	-0.3353	-0.1295	0.4771	0.1035	-0.0688	0.3389	0.0312	0.364	5.6506	220.1499	146.0537
6	3.8577	2.1828	2.913	1.4233	0.824	5.9102	-0.0854	-0.5066	0.2821	1.4996	-0.4545	0.0893	-0.5546	-0.5013	0.151	1.1661	-0.1896	0.0964	0.18	-0.0105	0.6724	20.3453	232.4167	177.0418
7	4.7735	-0.9536	-0.0388	2.4586	-0.4202	2.645	0.329	-0.1813	0.1322	0.1008	-0.4681	-0.583	0.2632	0.0328	-0.0225	0.2221	-0.0369	-0.0327	0.3083	0.0302	0.2742	23.4245	215.5547	174.0919
8	0.5703	-1.273	-0.2378	4.7672	-3.5091	8.8364	-0.8056	0.6749	-0.2041	0.3194	-0.2733	-0.1418	1.2167	0.236	-0.1741	0.5829	0.2007	-0.151	0.7248	-0.2181	0.8756	32.9846	204.8482	168.3535
9	0.1594	0.8766	-0.5616	4.7744	-3.1679	2.1336	-0.6183	-0.4008	0.3346	-0.9971	-0.336	0.0258	-0.0528	-0.528	-0.342	0.1794	-0.0283	-0.1444	0.4336	-0.1302	0.201	19.3555	217.8914	164.2869
10	3.1982	2.4216	-0.3805	4.7534	-0.726	7.397	0.6953	-0.5967	0.1633	0.0743	0.5139	-0.2201	-1.403	-0.2041	-0.5119	0.4633	-0.051	-0.0203	0.3317	-0.0373	0.5229	16.6711	227.2575	164.9121
11	7.0322	-2.0329	0.281	6.7913	-2.1153	6.5252	-0.0508	0.0988	2.1139	-0.3695	-0.4504	-1.0136	-1.3044	0.1162	0.2552	0.5719	-0.183	0.0111	0.3662	-0.0591	0.4797	27.9792	229.4511	168.9833
12	2.002	0.851	1.0845	1.1624	0.2146	3.036	-0.5729	0.3371	-0.0606	-0.4067	0.4191	-0.265	-0.1982	1.3029	0.1362	0.2703	-0.0236	0.0775	0.3234	0.0645	0.3572	28.4657	220.7539	157.7052
13	2.8303	-1.1077	1.3561	0.4923	-0.7949	2.924	-0.2056	-0.6384	0.1805	0.0818	0.1029	-0.1226	0.0353	-0.1827	0.2478	0.2839	-0.0648	-0.049	0.5301	0.0498	0.346	31.6999	217.3721	172.8453
14	6.0222	-1.6558	0.2217	5.1149	0.642	4.2251	-0.0113	-0.4626	0.6352	-0.0485	-0.078	-0.2631	-0.6368	0.6002	0.0394	0.336	-0.1139	-0.0705	0.5943	-0.0895	0.41	19.5266	220.0159	193.4825
15	6.3887	-1.8333	-1.6902	6.0849	2.5524	1.6094	0.4084	0.6189	0.038	-1.1344	-0.3176	1.2145	-0.4371	-0.783	0.1418	0.3139	0.0466	-0.0692	0.5909	-0.0461	0.2554	12.0985	221.3829	183.5414
16	6.4476	1.4908	-0.5605	5.8083	-2.8157	8.6848	0.192	0.4245	-0.2078	1.374	-0.5379	-0.4753	0.4942	-0.7155	0.3029	0.4011	-0.0287	-0.0755	0.2969	-0.0897	0.4317	17.7126	208.1251	187.6736
17	6.3751	0.8234	1.765	1.1417	0.1527	5.9354	0.1497	-0.6254	0.5767	0.33	-0.2908	0.328	0.0893	-1.2966	0.1534	0.2108	-0.023	0.023	0.6556	-0.0747	0.3539	7.4626	216.2005	190.8069
18	5.7237	0.2096	-1.3681	2.4716	-3.1032	4.1082	-0.0584	-0.0819	0.9171	1.4206	0.0992	-0.754	-0.9921	0.5184	0.3848	0.7154	0.1807	-0.1826	0.6699	-0.3055	0.6533	15.2509	227.2724	197.7029
19	1.1862	1.2691	0.6989	1.7401	-0.0215	1.8457	0.079	1.4762	-0.2548	-0.4925	0.6364	0.6579	-0.0259	-0.788	0.64	0.2507	-0.0327	-0.1323	1.3904	0.123	0.6431	-1.3896	209.8184	162.3127
20	2.8921	-0.0447	-0.0324	4.4549	-0.9662	3.9099	-0.3002	-0.0902	-0.0172	0.0722	-0.0116	-0.2278	0.2701	0.0212	0.368	0.3835	-0.1203	-0.0168	0.245	0.0115	0.2969	15.9683	208.34	163.8501
21	2.3206	-0.0491	0.0111	3.1266	0.2517	2.2927	0.3594	1.5006	-0.1782	-0.0202	-0.9262	-0.0762	-0.0151	-0.0323	-0.1002	0.3963	0.0876	-0.1401	0.5697	-0.0119	0.3247	19.8031	206.4365	171.6424
22	6.228	1.617	0.2308	2.9241	-2.5602	7.2813	0.2044	-0.0559	0.1994	0.2345	0.4348	0.705	-0.1919	-1.9378	-0.0772	0.3069	0.0919	0.0184	0.5718	-0.0574	0.5744	4.3389	213.0501	174.324
23	6.4908	0.3877	0.3853	5.5952	1.8606	4.3214	0.1413	-1.2827	-0.0504	-0.1981	-0.3157	0.3329	1.1401	-0.9712	-0.0675	0.3592	-0.1658	0.0302	0.3492	0.0939	0.4134	7.6835	201.7278	174.8153
24	2.6304	-1.7279	-1.7971	1.7096	1.2018	3.344	0.4117	0.3602	-0.5936	-0.7814	-0.3479	0.2103	0.1647	-0.519	0.1605	0.3858	-0.1866	0.0451	0.3615	-0.0712	0.3311	14.7376	200.0754	164.4634

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 12 THROUGH 39 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 40 THROUGH 53 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 54 THROUGH 62 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 63 THROUGH 82 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 83 THROUGH 103 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 12 THROUGH 20 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 21 THROUGH 39 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 40 THROUGH 46 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 47 THROUGH 53 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 54 THROUGH 62 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 63 THROUGH 72 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 73 THROUGH 84 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 85 THROUGH 103 )
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESID 10 THROUGH 40 )
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESID 41 THROUGH 53 )
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESID 54 THROUGH 62 )
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESID 63 THROUGH 92 )
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESID 93 THROUGH 103 )
19	X-RAY DIFFRACTION	19	CHAIN D AND (RESID 12 THROUGH 20 )
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESID 21 THROUGH 39 )
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESID 40 THROUGH 53 )
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESID 54 THROUGH 62 )
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESID 63 THROUGH 84 )
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESID 85 THROUGH 103 )

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