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- PDB-6k5s: Crystal structure of the Helical domain of S. pombe Tbf1 -

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Basic information

Entry
Database: PDB / ID: 6k5s
TitleCrystal structure of the Helical 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: 1.904 Å
AuthorsZhou, Y.Z. / Wang, N.N. / Zhao, Y.C. / Zeng, Z.X.
CitationJournal: To Be Published
Title: Crystal structure of the Helical 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 1.1Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: Telomeric DNA-binding factor trf1
B: Telomeric DNA-binding factor trf1
C: Telomeric DNA-binding factor trf1
D: Telomeric DNA-binding factor trf1


Theoretical massNumber of molelcules
Total (without water)102,0774
Polymers102,0774
Non-polymers00
Water8,827490
1
A: Telomeric DNA-binding factor trf1

C: Telomeric DNA-binding factor trf1


Theoretical massNumber of molelcules
Total (without water)51,0392
Polymers51,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area1560 Å2
ΔGint-21 kcal/mol
Surface area21520 Å2
MethodPISA
2
B: Telomeric DNA-binding factor trf1
D: Telomeric DNA-binding factor trf1


Theoretical massNumber of molelcules
Total (without water)51,0392
Polymers51,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-20 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.498, 80.639, 77.367
Angle α, β, γ (deg.)111.450, 94.640, 92.050
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Telomeric DNA-binding factor trf1


Mass: 25519.293 Da / Num. of mol.: 4
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.: 490 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: 0.2M Ammonium citrate tribasic Ph7.0, 20%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 65194 / % possible obs: 97.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 19.21 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.818 / Rrim(I) all: 0.077 / Net I/σ(I): 23.68
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.432 / Num. unique obs: 6438 / CC1/2: 0.903 / Χ2: 0.739 / % possible all: 96.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data scaling
SOLVEphasing
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.904→38.297 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 33.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 3067 4.94 %
Rwork0.221 59041 -
obs0.2237 62108 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.74 Å2 / Biso mean: 26.8388 Å2 / Biso min: 4.91 Å2
Refinement stepCycle: final / Resolution: 1.904→38.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 0 490 7380
Biso mean---27.51 -
Num. residues----870
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9042-1.93390.3308730.28511519159251
1.9339-1.96560.3215950.28362010210571
1.9656-1.99950.33631220.26312194231676
1.9995-2.03590.28911340.25762416255082
2.0359-2.0750.27391460.25312527267388
2.075-2.11740.30071450.25222740288594
2.1174-2.16340.28571500.24232813296397
2.1634-2.21370.31051390.24712839297897
2.2137-2.26910.31841280.23622917304597
2.2691-2.33040.27571390.22812794293398
2.3304-2.3990.3381490.23792843299297
2.399-2.47640.32211520.22142826297898
2.4764-2.56490.28671380.21912888302698
2.5649-2.66760.27181530.222806295998
2.6676-2.78890.28731590.23272883304298
2.7889-2.93590.28841350.23782864299998
2.9359-3.11980.26541460.23372856300298
3.1198-3.36060.26121550.21742861301698
3.3606-3.69850.2411650.20142844300998
3.6985-4.23310.26641500.18222902305299
4.2331-5.33090.21861530.19132858301199
5.3309-38.30480.26821410.20742841298297

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