PDB-4xht: Crystal structure of Timeless_PAB domain native form

ID or keywords:

Entry

Database: PDB / ID: 4xht

Title

Crystal structure of Timeless_PAB domain native 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 / cellular response to cisplatin / cell cycle phase transition / 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 /

MOLECULAR REPLACEMENT / Resolution: 1.651 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
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine / struct_ncs_dom_lim Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_method_to_determine_struct / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4xht.cif.gz	167.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4xht.ent.gz	133.2 KB	Display	PDB format
PDBx/mmJSON format	4xht.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4xht_validation.pdf.gz	448.7 KB	Display	wwPDB validaton report
Full document	4xht_full_validation.pdf.gz	451.6 KB	Display
Data in XML	4xht_validation.xml.gz	18.3 KB	Display
Data in CIF	4xht_validation.cif.gz	26.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xh/4xht ftp://data.pdbj.org/pub/pdb/validation_reports/xh/4xht	HTTPS FTP

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Related structure data

Related structure data	4xhuC 4xhwSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4xhw-1 1t4e-d 3uf4-d 4qwq-d 3h8h-4 2qnd-2 1a1a-d 5gl6-1 1mvk-1 1a08-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

C: Protein timeless homolog

B: Protein timeless homolog

D: Protein timeless homolog

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

Unit cell

Length a, b, c (Å)	66.668, 100.596, 149.554
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
2	1	CHAIN B
3	1	CHAIN C
4	1	CHAIN D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-ID	Beg auth comp-ID	Beg label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	ASN	ASN	CHAIN A	A	A	1005 - 1098	10 - 103
2	GLU	GLU	CHAIN B	B	C	1004 - 1098	9 - 103
3	ASN	ASN	CHAIN C	C	B	1005 - 1098	10 - 103
4	LEU	LEU	CHAIN D	D	D	1006 - 1098	11 - 103

#1: Protein	Protein timeless homolog / hTIM Mass: 11519.938 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
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.9 %
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: 1.06997 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: 1.06997 Å / Relative weight: 1
Reflection	Resolution: 1.65→26.34 Å / Num. obs: 59619 / % possible obs: 98.4 % / Redundancy: 6.3 % / R_merge(I) obs: 0.071 / Net I/σ(I): 29.65
Reflection shell	Resolution: 1.65→1.68 Å / % possible obs: 100 % / Redundancy: 6.3 % / R_merge(I) obs: 0.431 / Mean I/σ(I) obs: 4.64 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4XHW

4xhw

Resolution: 1.651→26.338 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2057	1998	3.35 %
R_work	0.1854	57608	-
obs	0.1861	59606	98.39 %

Solvent computation

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

Displacement parameters

B_iso max: 126.18 Å² / B_iso mean: 37.5269 Å² / B_iso min: 18.41 Å²

Refinement step

Cycle: final / Resolution: 1.651→26.338 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2877	0	0	322	3199
B_iso mean	-	-	-	44.67	-
Num. residues	-	-	-	-	369

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2981
X-RAY DIFFRACTION	f_angle_d	1.09	4052
X-RAY DIFFRACTION	f_chiral_restr	0.046	447
X-RAY DIFFRACTION	f_plane_restr	0.007	550
X-RAY DIFFRACTION	f_dihedral_angle_d	14.916	1147

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1732	X-RAY DIFFRACTION	7.17	TORSIONAL
1	2	B	1732	X-RAY DIFFRACTION	7.17	TORSIONAL
1	3	C	1732	X-RAY DIFFRACTION	7.17	TORSIONAL
1	4	D	1732	X-RAY DIFFRACTION	7.17	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6514-1.6926	0.2676	128	0.226	3714	3842	90
1.6926-1.7384	0.2285	143	0.2108	4144	4287	100
1.7384-1.7895	0.2452	143	0.2027	4118	4261	100
1.7895-1.8473	0.1876	144	0.1874	4140	4284	100
1.8473-1.9133	0.2123	145	0.1859	4145	4290	100
1.9133-1.9899	0.1946	144	0.1835	4153	4297	100
1.9899-2.0804	0.2188	145	0.1867	4178	4323	100
2.0804-2.19	0.1845	144	0.1779	4131	4275	100
2.19-2.3272	0.1984	144	0.1787	4178	4322	100
2.3272-2.5067	0.22	144	0.1905	4168	4312	100
2.5067-2.7587	0.2426	146	0.2009	4198	4344	100
2.7587-3.1574	0.2426	147	0.2145	4224	4371	100
3.1574-3.9758	0.1786	145	0.1673	4199	4344	99
3.9758-26.3414	0.1888	136	0.1735	3918	4054	89

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	0.0695	-0.0562	0.0959	0.3288	-0.2216	0.3782	0.2993	0.3339	-0.3082	-0.897	0.1488	-0.0662	0.936	0.2924	0.2591	0.6831	0.1199	0.0093	0.3484	-0.1534	0.4371	-12.1363	-31.999	-27.8762
2	0.3091	-0.1022	0.1146	0.0546	-0.1477	0.3088	0.0703	0.2318	0.1839	-0.0924	-0.1129	-0.0221	0.0039	0.1893	-0.0001	0.2209	0.0235	0.0009	0.3155	-0.0052	0.2685	-9.9918	-15.4917	-24.5928
3	0.0219	0.1448	0.0596	0.0912	0.375	0.7014	-0.1704	0.0289	0.3985	-0.281	0.1842	0.1749	-0.188	0.265	-0.0001	0.296	-0.0108	0.0134	0.2814	0.0111	0.3411	-7.9308	-11.9145	-16.3621
4	0.1142	-0.0266	0.1159	0.2046	-0.0055	0.1201	-0.0133	-0.0241	0.0743	0.2463	0.0242	0.1486	0.5785	-0.0915	0.0002	0.3808	-0.0001	0.0345	0.2101	-0.027	0.3121	-17.0151	-27.322	-15.4156
5	0.7261	-0.0361	0.4426	0.1057	-0.0662	0.3377	0.0314	0.3062	-0.5378	-0.0474	-0.0645	-0.1842	0.7912	0.9194	0.0017	0.4261	0.1565	0.0012	0.2967	-0.0445	0.3392	-5.4001	-29.3815	-19.5315
6	0.2165	-0.1433	0.1396	0.3553	0.1881	0.2358	0.0838	0.0383	-0.0681	0.1735	-0.0248	-0.1109	-0.0258	0.4438	0.0002	0.2416	0.0411	0.0145	0.3281	0.0195	0.2397	-3.279	-18.9889	-11.9401
7	0.0087	0.0421	0.0905	0.0709	-0.0381	0.1743	-0.0714	0.6052	-0.1022	-0.1426	0.1169	-0.3679	-0.0468	0.2882	0.0002	0.2216	0.0425	0.0329	0.4657	0.0101	0.2216	-2.0612	-17.8458	-28.8332
8	0.0665	-0.1142	-0.0039	0.3338	-0.1229	0.0775	0.0935	-0.9107	-0.2632	-0.0447	0.093	0.7684	-0.4411	-0.3257	-0.0024	0.3099	0.0945	0.1158	0.78	0.0295	0.457	-34.2909	-9.1885	-12.7443
9	0.2431	-0.4299	0.2964	0.8467	-0.2431	0.374	0.0034	-0.16	-0.0475	0.0635	-0.0553	-0.0545	-0.107	-0.2755	-0.0012	0.271	0.0337	0.0209	0.1993	0.0012	0.257	-17.4217	-8.236	-14.2976
10	0.2466	-0.1551	-0.366	0.3154	-0.1259	0.744	0.2563	-0.3731	-0.4238	0.1106	-0.2252	-0.6361	-0.2629	-0.0593	-0.0008	0.3127	0.0194	-0.0217	0.2818	0.0289	0.3601	-12.5765	-5.5675	-21.6186
11	0.114	-0.097	0.0672	0.0728	-0.0426	0.1093	-0.0099	0.3158	-0.3727	0.1368	0.0071	0.1189	-0.0526	-0.9029	0	0.2432	0.039	-0.0036	0.4337	-0.0526	0.3181	-29.0739	-12.7554	-24.7085
12	0.1335	0.1374	0.471	0.4359	-0.1707	3.9242	0.2487	-0.0604	0.2529	0.2672	0.19	0.4828	-0.3908	-2.3548	0.4896	0.3135	0.373	0.0569	0.4155	-0.0236	0.3224	-30.7239	-2.0875	-20.2282
13	0.2825	0.1956	-0.3158	0.4009	0.0214	0.2939	-0.1374	0.1748	0.1027	-0.205	0.2	-0.0588	-0.5523	-0.083	0.0002	0.3781	0.0725	-0.0066	0.2498	0.0021	0.2356	-19.3426	-0.2071	-26.2655
14	0.5839	0.1205	0.4435	0.0295	0.0419	0.4999	0.1288	-0.866	0.2388	0.3768	-0.2774	0.189	-0.1178	-0.6481	-0.0155	0.3983	0.0591	-0.0023	0.2831	-0.0252	0.2519	-19.659	-0.7723	-9.6145
15	0.0365	-0.0709	0.0972	0.2998	-0.0641	0.5029	0.3561	-0.7211	0.1476	1.065	0.2163	-0.1614	0.4934	0.6081	0.0107	0.5787	-0.0263	-0.0549	0.3639	-0.0528	0.2942	-13.9037	-12.8362	12.8531
16	0.9346	0.4373	-0.5668	0.5016	-0.0966	0.3857	0.1364	0.5426	0.5418	0.0865	0.1722	0.3197	-0.3975	-0.1708	0.0389	0.3132	0.0087	0.057	0.2287	0.0529	0.3229	-26.2371	-12.4536	1.117
17	0.155	-0.234	-0.1659	0.1986	0.0541	0.3813	-0.2837	0.2296	-0.011	-0.3411	0.1309	0.0374	0.0061	-0.3859	-0.0007	0.3041	-0.0631	0.0021	0.2956	0.0058	0.2542	-24.4584	-18.5656	-5.7775
18	0.0578	-0.033	0.0034	0.1549	0.0205	0.1076	-0.0018	-0.0811	0.0738	-0.029	0.1599	-0.3225	-0.0897	0.5092	0	0.3128	-0.0219	0.0282	0.2784	-0.0216	0.2825	-10.7795	-15.8108	-0.4385
19	0.7025	0.1666	0.2265	0.0982	0.1015	0.1408	0.0938	-0.8363	-0.2854	0.4943	-0.1836	-0.0558	0.4912	0.1316	-0.0195	0.4194	0.0331	0.024	0.2491	0.0646	0.2811	-16.6477	-22.3325	8.1362
20	0.656	-0.7157	-0.9603	1.3647	1.5589	2.5105	-0.2367	0.3583	-0.6319	0.1371	-0.3907	0.1657	0.7691	-0.6161	-0.0745	0.5459	-0.0609	0.1118	0.1929	-0.0429	0.3824	-20.0415	-29.1007	-3.9134
21	-0.0067	-0.0334	-0.0272	0.1531	-0.2056	0.1109	-0.0823	0.2432	-0.1915	-0.029	0.0489	0.2481	0.3349	-0.4265	0.0001	0.3092	-0.058	0.0424	0.2507	-0.007	0.3042	-25.1301	-24.0908	-1.3333
22	0.0767	-0.1163	-0.0065	0.1629	-0.036	0.1091	0.1191	-0.6999	0.2839	0.523	-0.1111	0.5735	0.2169	-0.2654	-0.0011	0.3961	-0.0079	0.1207	0.3202	-0.0064	0.3195	-30.4675	-15.867	8.4357
23	0.5258	0.2246	0.581	3.5299	-0.0926	0.7128	0.0309	1.6702	0.0764	-0.9641	0.154	0.1421	-0.408	-0.3561	-0.0411	0.3814	0.0416	0.0366	0.777	0.0528	0.3376	-10.7298	-10.5948	-50.8804
24	0.2438	-0.0393	0.0684	0.1339	0.0429	0.4842	0.0082	0.0414	-0.4633	0.0377	-0.101	-0.0452	0.1325	0.336	-0.0101	0.233	0.04	0.0328	0.3487	-0.0548	0.3843	-14.7173	-22.8019	-40.3535
25	0.2458	0.1432	0.0407	0.2373	0.2693	0.5703	-0.0491	-0.0236	-0.4557	0.2106	-0.082	0.2057	0.3617	0.4078	-0.0827	0.3018	0.0245	0.0267	0.3001	-0.022	0.3727	-20.9827	-21.7835	-34.6572
26	0.0937	-0.0504	-0.0487	0.0973	-0.1355	0.1613	0.2031	-0.194	-0.0489	-0.0616	0.0301	-0.0517	-0.5086	-0.2042	0.0002	0.2957	0.0283	0.032	0.368	-0.0323	0.2432	-15.3964	-7.742	-38.0197
27	0.4185	-0.3863	0.1075	0.4571	0.0331	0.1839	0.0438	0.3312	0.0321	-0.0716	-0.1445	0.1575	-0.1933	-0.474	0.0004	0.1745	0.0236	-0.0256	0.4192	-0.0541	0.2497	-25.7385	-14.0842	-40.829
28	0.0159	-0.0638	-0.0296	0.157	0.122	0.1693	-0.0819	1.015	-0.4718	-0.6385	-0.0966	0.2014	0.2787	-0.6119	-0.0016	0.4616	-0.0426	0.0714	0.4438	-0.1973	0.518	-21.0331	-26.9987	-46.7888

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1005 THROUGH 1015 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 1016 THROUGH 1034 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 1035 THROUGH 1048 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 1049 THROUGH 1057 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 1058 THROUGH 1067 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 1068 THROUGH 1087 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 1088 THROUGH 1098 )
8	X-RAY DIFFRACTION	8	CHAIN C AND (RESID 1005 THROUGH 1015 )
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESID 1016 THROUGH 1034 )
10	X-RAY DIFFRACTION	10	CHAIN C AND (RESID 1035 THROUGH 1048 )
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESID 1049 THROUGH 1057 )
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESID 1058 THROUGH 1067 )
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESID 1068 THROUGH 1087 )
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESID 1088 THROUGH 1098 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 1004 THROUGH 1015 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 1016 THROUGH 1034 )
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 1035 THROUGH 1048 )
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 1049 THROUGH 1057 )
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESID 1058 THROUGH 1067 )
20	X-RAY DIFFRACTION	20	CHAIN B AND (RESID 1068 THROUGH 1077 )
21	X-RAY DIFFRACTION	21	CHAIN B AND (RESID 1078 THROUGH 1087 )
22	X-RAY DIFFRACTION	22	CHAIN B AND (RESID 1088 THROUGH 1098 )
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESID 1006 THROUGH 1015 )
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESID 1016 THROUGH 1033 )
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESID 1034 THROUGH 1048 )
26	X-RAY DIFFRACTION	26	CHAIN D AND (RESID 1049 THROUGH 1057 )
27	X-RAY DIFFRACTION	27	CHAIN D AND (RESID 1058 THROUGH 1082 )
28	X-RAY DIFFRACTION	28	CHAIN D AND (RESID 1083 THROUGH 1098 )

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