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- PDB-8x6e: crystal structure of the N-terminal TBF1 -

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Basic information

Entry
Database: PDB / ID: 8x6e
Titlecrystal structure of the N-terminal TBF1
ComponentsProtein TBF1
KeywordsDNA BINDING PROTEIN / telomere / DNA damage response / gene transcription
Function / homology
Function and homology information


snoRNA transcription by RNA polymerase II / chromatin insulator sequence binding / telomere maintenance via telomere lengthening / double-stranded telomeric DNA binding / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling ...snoRNA transcription by RNA polymerase II / chromatin insulator sequence binding / telomere maintenance via telomere lengthening / double-stranded telomeric DNA binding / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / protein homodimerization activity / nucleus
Similarity search - Function
: / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00002083763 Å
AuthorsGao, Y. / Niu, L.W.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Structural study of yeast TBF1 protein
Authors: Gao, Y. / Niu, L.W.
History
DepositionNov 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein TBF1


Theoretical massNumber of molelcules
Total (without water)35,4191
Polymers35,4191
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.014, 168.635, 39.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Protein TBF1


Mass: 35418.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: TBF1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q02457
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris, pH 8.0, 25 % v/v PEG 400, 10% 0.1 M Magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→42.375 Å / Num. obs: 23207 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 35.7409409771 Å2 / CC1/2: 1 / Net I/σ(I): 28.2
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 1674 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.00002083763→42.3746589575 Å / SU ML: 0.247029643467 / Cross valid method: FREE R-VALUE / σ(F): 1.33132083659 / Phase error: 26.9899985566
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236303942258 1127 4.94450050454 %
Rwork0.212709230823 21666 -
obs0.213976070355 22793 98.3219739453 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.7252012689 Å2
Refinement stepCycle: LAST / Resolution: 2.00002083763→42.3746589575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 0 114 2449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003603665414792377
X-RAY DIFFRACTIONf_angle_d0.577682096643217
X-RAY DIFFRACTIONf_chiral_restr0.0378952380688373
X-RAY DIFFRACTIONf_plane_restr0.00401815387392412
X-RAY DIFFRACTIONf_dihedral_angle_d12.5504958781448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.00002083763-2.0910.3357430892211550.3073549632862674X-RAY DIFFRACTION99.2631578947
2.091-2.20130.3329592322731290.2520496828382699X-RAY DIFFRACTION100
2.2013-2.33920.3708504835441480.3055011366892373X-RAY DIFFRACTION87.595552467
2.3392-2.51980.2444165525811180.2322493402212723X-RAY DIFFRACTION100
2.5198-2.77330.2364691767191530.2343673540642698X-RAY DIFFRACTION99.9649368864
2.7733-3.17450.2837409864771380.2302433165172758X-RAY DIFFRACTION100
3.1745-3.99910.2592524442591280.202749325932810X-RAY DIFFRACTION99.6607869742
3.9991-42.37465895750.1726458028621580.1777759765122931X-RAY DIFFRACTION100

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