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- PDB-5mqi: Crystal structure of the N-terminal domain of human Timeless -

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Basic information

Entry
Database: PDB / ID: 5mqi
TitleCrystal structure of the N-terminal domain of human Timeless
ComponentsProtein timeless homolog,Protein timeless homolog
KeywordsREPLICATION / DNA Replication / genomic stability
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 / enzyme activator activity / circadian rhythm / regulation of circadian rhythm / 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 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 / Resolution: 1.847 Å
AuthorsHolzer, S. / Kilkenny, M.L. / Pellegrini, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust104641/Z/14/Z United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Crystal structure of the N-terminal domain of human Timeless and its interaction with Tipin.
Authors: Holzer, S. / Degliesposti, G. / Kilkenny, M.L. / Maslen, S.L. / Matak-Vinkovic, D. / Skehel, M. / Pellegrini, L.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3May 31, 2017Group: Database references
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein timeless homolog,Protein timeless homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2435
Polymers43,8591
Non-polymers3844
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-41 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.008, 71.337, 185.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-40-

ARG

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Components

#1: Protein Protein timeless homolog,Protein timeless homolog / hTIM / hTIM


Mass: 43858.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The recombinant version of the N-terminal domain of human Timeless used for X-ray crystal structure determination carried an internal deletion of amino acids 239 to 330, which were replaced ...Details: The recombinant version of the N-terminal domain of human Timeless used for X-ray crystal structure determination carried an internal deletion of amino acids 239 to 330, which were replaced with the artificial linker sequence GSTGST.
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMELESS, TIM, TIM1, TIMELESS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNS1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: reservoir solution: 20% (w/v) PEG 3350, 200 mM Na2SO4 protein solution: 8.5 mg/mL, 150 mM KCl, 25 mM Heps pH 7.2, 1 mM TCEP 200 nL protein solution and 200 nL of reservoir solution were mixed.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.847→49.22 Å / Num. obs: 36572 / % possible obs: 94.4 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.6
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.645 / % possible all: 87.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 1.847→43.456 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 20.41
RfactorNum. reflection% reflection
Rfree0.1974 3474 5.26 %
Rwork0.1702 --
obs0.1716 36568 88.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.847→43.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 20 161 2996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152929
X-RAY DIFFRACTIONf_angle_d1.2883972
X-RAY DIFFRACTIONf_dihedral_angle_d12.2481761
X-RAY DIFFRACTIONf_chiral_restr0.069439
X-RAY DIFFRACTIONf_plane_restr0.009511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8471-1.87240.3041210.30112158X-RAY DIFFRACTION76
1.8724-1.89910.34531720.29372643X-RAY DIFFRACTION93
1.8991-1.92750.28591700.28182526X-RAY DIFFRACTION92
1.9275-1.95760.28791620.26712581X-RAY DIFFRACTION92
1.9576-1.98970.28311380.24612572X-RAY DIFFRACTION90
1.9897-2.0240.261380.23632540X-RAY DIFFRACTION91
2.024-2.06080.24021360.20882644X-RAY DIFFRACTION91
2.0608-2.10040.22781390.20262521X-RAY DIFFRACTION91
2.1004-2.14330.24191380.1922633X-RAY DIFFRACTION91
2.1433-2.18990.19191360.18882463X-RAY DIFFRACTION89
2.1899-2.24080.23041340.18312550X-RAY DIFFRACTION88
2.2408-2.29690.19991320.17082524X-RAY DIFFRACTION91
2.2969-2.3590.20991470.17332595X-RAY DIFFRACTION90
2.359-2.42840.20351300.1682484X-RAY DIFFRACTION89
2.4284-2.50680.20411160.16932552X-RAY DIFFRACTION89
2.5068-2.59630.21611690.17452552X-RAY DIFFRACTION90
2.5963-2.70030.18791170.16242507X-RAY DIFFRACTION89
2.7003-2.82320.18251220.16742409X-RAY DIFFRACTION86
2.8232-2.9720.2131570.17342502X-RAY DIFFRACTION89
2.972-3.15810.24341280.18422488X-RAY DIFFRACTION88
3.1581-3.40190.22531600.18442451X-RAY DIFFRACTION87
3.4019-3.74410.16061640.15632418X-RAY DIFFRACTION86
3.7441-4.28540.1789990.14482416X-RAY DIFFRACTION85
4.2854-5.39760.12421370.13282456X-RAY DIFFRACTION87
5.3976-43.46850.21081120.1682448X-RAY DIFFRACTION86

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