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- PDB-6t9q: Crystal structure of the second, C-terminal repeat of the DNA-bin... -

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Basic information

Entry
Database: PDB / ID: 6t9q
TitleCrystal structure of the second, C-terminal repeat of the DNA-binding domain of human TImeless
ComponentsProtein timeless homolog
KeywordsREPLICATION / DNA-binding / 3-helix bundle / tandem repeat
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 ...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 / positive regulation of double-strand break repair via homologous recombination / morphogenesis of an epithelium / lung development / regulation of circadian rhythm / 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 / nucleus / identical protein binding
Similarity search - Function
Timeless, C-terminal / Timeless PAB domain / Timeless / Timeless, N-terminal / Timeless protein
Similarity search - Domain/homology
Protein timeless homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsPellegrini, L. / Holzer, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust104641/Z/14/Z United Kingdom
CitationJournal: Embo J. / Year: 2020
Title: Timeless couples G-quadruplex detection with processing by DDX11 helicase during DNA replication.
Authors: Lerner, L.K. / Holzer, S. / Kilkenny, M.L. / Svikovic, S. / Murat, P. / Schiavone, D. / Eldridge, C.B. / Bittleston, A. / Maman, J.D. / Branzei, D. / Stott, K. / Pellegrini, L. / Sale, J.E.
History
DepositionOct 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein timeless homolog


Theoretical massNumber of molelcules
Total (without water)7,8761
Polymers7,8761
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.407, 55.407, 41.659
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Protein timeless homolog / hTIM


Mass: 7876.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The DP dipeptide at the start of the sequence is part of the leftover of the expression tag after protease cleavage
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 / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 200mM Sodium formate 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.15→31.46 Å / Num. obs: 25072 / % possible obs: 96.33 % / Redundancy: 4.2 % / Biso Wilson estimate: 11.3 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.1377 / Rpim(I) all: 0.06851 / Rrim(I) all: 0.1543 / Net I/σ(I): 6.82
Reflection shellResolution: 1.15→1.191 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.4873 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 1920 / CC1/2: 0.464 / Rpim(I) all: 0.4274 / Rrim(I) all: 0.6505 / % possible all: 74.84

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.16-3549refinement
RefinementMethod to determine structure: SAD / Resolution: 1.15→31.46 Å / SU ML: 0.1255 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.4928
RfactorNum. reflection% reflection
Rfree0.1547 1267 5.07 %
Rwork0.128 --
obs0.1294 24985 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.72 Å2
Refinement stepCycle: LAST / Resolution: 1.15→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms516 0 0 132 648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078534
X-RAY DIFFRACTIONf_angle_d0.9639715
X-RAY DIFFRACTIONf_chiral_restr0.067580
X-RAY DIFFRACTIONf_plane_restr0.007291
X-RAY DIFFRACTIONf_dihedral_angle_d11.7066211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.20.35191100.2642051X-RAY DIFFRACTION75.82
1.2-1.250.21391280.18232539X-RAY DIFFRACTION93.28
1.25-1.320.17791320.13472708X-RAY DIFFRACTION98.61
1.32-1.40.15311380.11882710X-RAY DIFFRACTION99.82
1.4-1.510.16331320.11122755X-RAY DIFFRACTION99.93
1.51-1.660.1381560.09952719X-RAY DIFFRACTION99.93
1.66-1.90.15511540.10762726X-RAY DIFFRACTION99.83
1.9-2.390.12551560.11512734X-RAY DIFFRACTION99.93
2.39-31.460.1541610.13792776X-RAY DIFFRACTION99.66

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