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- PDB-8ynu: Crystal structure of the myb domain of S.pombe Tbf1 in the P222 s... -

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Basic information

Entry
Database: PDB / ID: 8ynu
TitleCrystal structure of the myb domain of S.pombe Tbf1 in the P222 space group
ComponentsTelomeric DNA-binding factor trf1
KeywordsDNA BINDING PROTEIN / Telomere binding protein
Function / homology
Function and homology information


chromosome, telomeric repeat region / telomere maintenance via telomere lengthening / double-stranded telomeric DNA binding / telomere maintenance / chromatin / 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
Telomeric DNA-binding factor trf1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsZhou, Y.Z. / Wu, Z.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structural and functional insights into yeast Tbf1 as an atypical telomeric repeat-binding factor.
Authors: Wu, Z. / Gu, X. / Zha, L. / Yang, Q. / Zhou, Y. / Zeng, Z.
History
DepositionMar 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomeric DNA-binding factor trf1
B: Telomeric DNA-binding factor trf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2153
Polymers18,1232
Non-polymers921
Water2,468137
1
A: Telomeric DNA-binding factor trf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1542
Polymers9,0611
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Telomeric DNA-binding factor trf1


Theoretical massNumber of molelcules
Total (without water)9,0611
Polymers9,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.393, 62.230, 86.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number16
Space group name H-MP222
Space group name HallP22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-501-

GOL

21A-657-

HOH

31B-536-

HOH

41B-547-

HOH

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Components

#1: Protein Telomeric DNA-binding factor trf1


Mass: 9061.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: trf1, SPBC19G7.13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6E434
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: 16% PEG 8000, 40mM Potassium phosphate dibasic, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97778 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 292977 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 20.63 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.031 / Rrim(I) all: 0.112 / Rsym value: 0.107 / Net I/σ(I): 36.28
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6.083 / Num. unique obs: 1114 / CC1/2: 0.937 / Rpim(I) all: 0.111 / Rrim(I) all: 0.396 / Rsym value: 0.38

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→43.39 Å / SU ML: 0.1717 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.7545 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.232 1133 5 %
Rwork0.1936 21547 -
obs0.1955 22680 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.35 Å2
Refinement stepCycle: LAST / Resolution: 1.76→43.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 6 137 1403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871283
X-RAY DIFFRACTIONf_angle_d0.88571718
X-RAY DIFFRACTIONf_chiral_restr0.0544185
X-RAY DIFFRACTIONf_plane_restr0.0042218
X-RAY DIFFRACTIONf_dihedral_angle_d19.762500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.840.2631380.23122606X-RAY DIFFRACTION98.42
1.84-1.940.23731400.19832659X-RAY DIFFRACTION99.89
1.94-2.060.22181390.19562650X-RAY DIFFRACTION99.89
2.06-2.220.23621400.19952671X-RAY DIFFRACTION99.86
2.22-2.450.25351400.19652679X-RAY DIFFRACTION99.86
2.45-2.80.23021420.20752700X-RAY DIFFRACTION99.79
2.8-3.530.24631420.19912722X-RAY DIFFRACTION99.76
3.53-43.390.21071520.1752860X-RAY DIFFRACTION99.08

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