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

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Basic information

Entry
Database: PDB / ID: 4xht
TitleCrystal structure of Timeless_PAB domain native form
ComponentsProtein timeless homolog
KeywordsREPLICATION / DNA damage response
Function / homology
Function and homology information


cellular response to bleomycin / detection of abiotic stimulus / replication fork arrest / cell cycle phase transition / replication fork protection complex / cellular response to cisplatin / cellular response to hydroxyurea / DNA replication checkpoint signaling / branching morphogenesis of an epithelial tube / positive regulation of double-strand break repair ...cellular response to bleomycin / detection of abiotic stimulus / replication fork arrest / cell cycle phase transition / replication fork protection complex / cellular response to cisplatin / cellular response to hydroxyurea / DNA replication checkpoint signaling / branching morphogenesis of an epithelial tube / positive regulation of double-strand break repair / replication fork processing / positive regulation of double-strand break repair via homologous recombination / lung development / morphogenesis of an epithelium / circadian rhythm / regulation of circadian rhythm / enzyme activator activity / site of double-strand break / Processing of DNA double-strand break ends / cell division / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / chromatin / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Timeless, C-terminal / Timeless-like, PAB domain / Timeless, N-terminal / Timeless / Timeless protein
Similarity search - Domain/homology
Protein timeless homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsXie, S. / Qian, C.
Funding support Hong Kong, 2items
OrganizationGrant numberCountry
General research council776313 Hong Kong
General research council775712 Hong Kong
CitationJournal: 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
DepositionJan 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein timeless homolog
C: Protein timeless homolog
B: Protein timeless homolog
D: Protein timeless homolog


Theoretical massNumber of molelcules
Total (without water)46,0804
Polymers46,0804
Non-polymers00
Water5,711317
1
A: Protein timeless homolog
B: Protein timeless homolog


Theoretical massNumber of molelcules
Total (without water)23,0402
Polymers23,0402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein timeless homolog
D: Protein timeless homolog


Theoretical massNumber of molelcules
Total (without water)23,0402
Polymers23,0402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A
21CHAIN B
31CHAIN C
41CHAIN D

NCS domain segments:

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

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNCHAIN AAA1005 - 109810 - 103
2GLUGLUCHAIN BBC1004 - 10989 - 103
3ASNASNCHAIN CCB1005 - 109810 - 103
4LEULEUCHAIN DDD1006 - 109811 - 103

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Components

#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 modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 25% PEG 3350, 200mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.06997 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06997 Å / Relative weight: 1
ReflectionResolution: 1.65→26.34 Å / Num. obs: 59619 / % possible obs: 98.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 29.65
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 4.64 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2057 1998 3.35 %
Rwork0.1854 57608 -
obs0.1861 59606 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.18 Å2 / Biso mean: 37.5269 Å2 / Biso min: 18.41 Å2
Refinement stepCycle: final / Resolution: 1.651→26.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 0 322 3199
Biso mean---44.67 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072981
X-RAY DIFFRACTIONf_angle_d1.094052
X-RAY DIFFRACTIONf_chiral_restr0.046447
X-RAY DIFFRACTIONf_plane_restr0.007550
X-RAY DIFFRACTIONf_dihedral_angle_d14.9161147
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1732X-RAY DIFFRACTION7.17TORSIONAL
12B1732X-RAY DIFFRACTION7.17TORSIONAL
13C1732X-RAY DIFFRACTION7.17TORSIONAL
14D1732X-RAY DIFFRACTION7.17TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6514-1.69260.26761280.2263714384290
1.6926-1.73840.22851430.210841444287100
1.7384-1.78950.24521430.202741184261100
1.7895-1.84730.18761440.187441404284100
1.8473-1.91330.21231450.185941454290100
1.9133-1.98990.19461440.183541534297100
1.9899-2.08040.21881450.186741784323100
2.0804-2.190.18451440.177941314275100
2.19-2.32720.19841440.178741784322100
2.3272-2.50670.221440.190541684312100
2.5067-2.75870.24261460.200941984344100
2.7587-3.15740.24261470.214542244371100
3.1574-3.97580.17861450.16734199434499
3.9758-26.34140.18881360.17353918405489
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.0695-0.05620.09590.3288-0.22160.37820.29930.3339-0.3082-0.8970.1488-0.06620.9360.29240.25910.68310.11990.00930.3484-0.15340.4371-12.1363-31.999-27.8762
20.3091-0.10220.11460.0546-0.14770.30880.07030.23180.1839-0.0924-0.1129-0.02210.00390.1893-0.00010.22090.02350.00090.3155-0.00520.2685-9.9918-15.4917-24.5928
30.02190.14480.05960.09120.3750.7014-0.17040.02890.3985-0.2810.18420.1749-0.1880.265-0.00010.296-0.01080.01340.28140.01110.3411-7.9308-11.9145-16.3621
40.1142-0.02660.11590.2046-0.00550.1201-0.0133-0.02410.07430.24630.02420.14860.5785-0.09150.00020.3808-0.00010.03450.2101-0.0270.3121-17.0151-27.322-15.4156
50.7261-0.03610.44260.1057-0.06620.33770.03140.3062-0.5378-0.0474-0.0645-0.18420.79120.91940.00170.42610.15650.00120.2967-0.04450.3392-5.4001-29.3815-19.5315
60.2165-0.14330.13960.35530.18810.23580.08380.0383-0.06810.1735-0.0248-0.1109-0.02580.44380.00020.24160.04110.01450.32810.01950.2397-3.279-18.9889-11.9401
70.00870.04210.09050.0709-0.03810.1743-0.07140.6052-0.1022-0.14260.1169-0.3679-0.04680.28820.00020.22160.04250.03290.46570.01010.2216-2.0612-17.8458-28.8332
80.0665-0.1142-0.00390.3338-0.12290.07750.0935-0.9107-0.2632-0.04470.0930.7684-0.4411-0.3257-0.00240.30990.09450.11580.780.02950.457-34.2909-9.1885-12.7443
90.2431-0.42990.29640.8467-0.24310.3740.0034-0.16-0.04750.0635-0.0553-0.0545-0.107-0.2755-0.00120.2710.03370.02090.19930.00120.257-17.4217-8.236-14.2976
100.2466-0.1551-0.3660.3154-0.12590.7440.2563-0.3731-0.42380.1106-0.2252-0.6361-0.2629-0.0593-0.00080.31270.0194-0.02170.28180.02890.3601-12.5765-5.5675-21.6186
110.114-0.0970.06720.0728-0.04260.1093-0.00990.3158-0.37270.13680.00710.1189-0.0526-0.902900.24320.039-0.00360.4337-0.05260.3181-29.0739-12.7554-24.7085
120.13350.13740.4710.4359-0.17073.92420.2487-0.06040.25290.26720.190.4828-0.3908-2.35480.48960.31350.3730.05690.4155-0.02360.3224-30.7239-2.0875-20.2282
130.28250.1956-0.31580.40090.02140.2939-0.13740.17480.1027-0.2050.2-0.0588-0.5523-0.0830.00020.37810.0725-0.00660.24980.00210.2356-19.3426-0.2071-26.2655
140.58390.12050.44350.02950.04190.49990.1288-0.8660.23880.3768-0.27740.189-0.1178-0.6481-0.01550.39830.0591-0.00230.2831-0.02520.2519-19.659-0.7723-9.6145
150.0365-0.07090.09720.2998-0.06410.50290.3561-0.72110.14761.0650.2163-0.16140.49340.60810.01070.5787-0.0263-0.05490.3639-0.05280.2942-13.9037-12.836212.8531
160.93460.4373-0.56680.5016-0.09660.38570.13640.54260.54180.08650.17220.3197-0.3975-0.17080.03890.31320.00870.0570.22870.05290.3229-26.2371-12.45361.117
170.155-0.234-0.16590.19860.05410.3813-0.28370.2296-0.011-0.34110.13090.03740.0061-0.3859-0.00070.3041-0.06310.00210.29560.00580.2542-24.4584-18.5656-5.7775
180.0578-0.0330.00340.15490.02050.1076-0.0018-0.08110.0738-0.0290.1599-0.3225-0.08970.509200.3128-0.02190.02820.2784-0.02160.2825-10.7795-15.8108-0.4385
190.70250.16660.22650.09820.10150.14080.0938-0.8363-0.28540.4943-0.1836-0.05580.49120.1316-0.01950.41940.03310.0240.24910.06460.2811-16.6477-22.33258.1362
200.656-0.7157-0.96031.36471.55892.5105-0.23670.3583-0.63190.1371-0.39070.16570.7691-0.6161-0.07450.5459-0.06090.11180.1929-0.04290.3824-20.0415-29.1007-3.9134
21-0.0067-0.0334-0.02720.1531-0.20560.1109-0.08230.2432-0.1915-0.0290.04890.24810.3349-0.42650.00010.3092-0.0580.04240.2507-0.0070.3042-25.1301-24.0908-1.3333
220.0767-0.1163-0.00650.1629-0.0360.10910.1191-0.69990.28390.523-0.11110.57350.2169-0.2654-0.00110.3961-0.00790.12070.3202-0.00640.3195-30.4675-15.8678.4357
230.52580.22460.5813.5299-0.09260.71280.03091.67020.0764-0.96410.1540.1421-0.408-0.3561-0.04110.38140.04160.03660.7770.05280.3376-10.7298-10.5948-50.8804
240.2438-0.03930.06840.13390.04290.48420.00820.0414-0.46330.0377-0.101-0.04520.13250.336-0.01010.2330.040.03280.3487-0.05480.3843-14.7173-22.8019-40.3535
250.24580.14320.04070.23730.26930.5703-0.0491-0.0236-0.45570.2106-0.0820.20570.36170.4078-0.08270.30180.02450.02670.3001-0.0220.3727-20.9827-21.7835-34.6572
260.0937-0.0504-0.04870.0973-0.13550.16130.2031-0.194-0.0489-0.06160.0301-0.0517-0.5086-0.20420.00020.29570.02830.0320.368-0.03230.2432-15.3964-7.742-38.0197
270.4185-0.38630.10750.45710.03310.18390.04380.33120.0321-0.0716-0.14450.1575-0.1933-0.4740.00040.17450.0236-0.02560.4192-0.05410.2497-25.7385-14.0842-40.829
280.0159-0.0638-0.02960.1570.1220.1693-0.08191.015-0.4718-0.6385-0.09660.20140.2787-0.6119-0.00160.4616-0.04260.07140.4438-0.19730.518-21.0331-26.9987-46.7888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1005 THROUGH 1015 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1016 THROUGH 1034 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1035 THROUGH 1048 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1049 THROUGH 1057 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1058 THROUGH 1067 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 1068 THROUGH 1087 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 1088 THROUGH 1098 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 1005 THROUGH 1015 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 1016 THROUGH 1034 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 1035 THROUGH 1048 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 1049 THROUGH 1057 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 1058 THROUGH 1067 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 1068 THROUGH 1087 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 1088 THROUGH 1098 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 1004 THROUGH 1015 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 1016 THROUGH 1034 )
17X-RAY DIFFRACTION17CHAIN B AND (RESID 1035 THROUGH 1048 )
18X-RAY DIFFRACTION18CHAIN B AND (RESID 1049 THROUGH 1057 )
19X-RAY DIFFRACTION19CHAIN B AND (RESID 1058 THROUGH 1067 )
20X-RAY DIFFRACTION20CHAIN B AND (RESID 1068 THROUGH 1077 )
21X-RAY DIFFRACTION21CHAIN B AND (RESID 1078 THROUGH 1087 )
22X-RAY DIFFRACTION22CHAIN B AND (RESID 1088 THROUGH 1098 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 1006 THROUGH 1015 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 1016 THROUGH 1033 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 1034 THROUGH 1048 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 1049 THROUGH 1057 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 1058 THROUGH 1082 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 1083 THROUGH 1098 )

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