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- PDB-6k5u: Crystal structure of the myb domain of S. pombe Tbf1 -

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Basic information

Entry
Database: PDB / ID: 6k5u
TitleCrystal structure of the myb domain of S. pombe Tbf1
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 (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.079 Å
AuthorsZhou, Y.Z. / Wang, N.N. / Zhao, Y.C. / Zeng, Z.X.
CitationJournal: To Be Published
Title: Crystal structure of the myb domain of S. pombe Tbf1
Authors: Zhou, Y.Z. / Wang, N.N. / Zhao, Y.C. / Zeng, Z.X.
History
DepositionMay 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)18,2322
Polymers18,2322
Non-polymers00
Water2,144119
1
A: Telomeric DNA-binding factor trf1


Theoretical massNumber of molelcules
Total (without water)9,1161
Polymers9,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Telomeric DNA-binding factor trf1


Theoretical massNumber of molelcules
Total (without water)9,1161
Polymers9,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.393, 105.393, 41.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

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Components

#1: Protein Telomeric DNA-binding factor trf1


Mass: 9116.227 Da / Num. of mol.: 2 / Mutation: L420M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: trf1, SPBC19G7.13 / Variant: 972 / ATCC 24843 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6E434
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsL420M is mutated and MET is modified to MSE.

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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: 3.17 Å3/Da / Density % sol: 61.14 %
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: 2.079→40 Å / Num. obs: 14514 / % possible obs: 100 % / Redundancy: 24.7 % / Biso Wilson estimate: 26.39 Å2 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.038 / Rrim(I) all: 0.189 / Χ2: 1.368 / Net I/σ(I): 32.455
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 23.4 % / Rmerge(I) obs: 0.873 / Num. unique obs: 696 / CC1/2: 0.964 / Rpim(I) all: 0.183 / Rrim(I) all: 0.893 / Χ2: 0.494 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.079→37.262 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.07
RfactorNum. reflection% reflection
Rfree0.2221 737 5.09 %
Rwork0.1894 --
obs0.1912 14482 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.07 Å2 / Biso mean: 29.0306 Å2 / Biso min: 13.44 Å2
Refinement stepCycle: final / Resolution: 2.079→37.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 0 119 1365
Biso mean---34.29 -
Num. residues----156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.079-2.23950.23561260.18192651277798
2.2395-2.46480.23441440.183727072851100
2.4648-2.82130.25651650.203927042869100
2.8213-3.55410.22721380.19827762914100
3.5541-37.2680.20171640.182429073071100

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