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- PDB-3kf6: Crystal structure of S. pombe Stn1-ten1 complex -

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Basic information

Entry
Database: PDB / ID: 3kf6
TitleCrystal structure of S. pombe Stn1-ten1 complex
Components
  • Protein stn1
  • Protein ten1
KeywordsSTRUCTURAL PROTEIN / OB fold / Chromosomal protein / DNA-binding / Nucleus / Telomere
Function / homology
Function and homology information


CST complex / telomere cap complex / chromosome, telomeric repeat region / single-stranded telomeric DNA binding / telomere capping / negative regulation of telomere maintenance via telomerase / nucleus
Similarity search - Function
CST complex subunit Ten1, fungal / Telomere capping, CST complex subunit / CST complex subunit Stn1, N-terminal / Telomere regulation protein Stn1 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Protein ten1 / Protein stn1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsSun, J. / Yu, E.Y. / Yang, Y.T. / Confer, L.A. / Sun, S.H. / Wan, K. / Lue, N.F. / Lei, M.
CitationJournal: Genes Dev. / Year: 2009
Title: Stn1-Ten1 is an Rpa2-Rpa3-like complex at telomeres.
Authors: Sun, J. / Yu, E.Y. / Yang, Y. / Confer, L.A. / Sun, S.H. / Wan, K. / Lue, N.F. / Lei, M.
History
DepositionOct 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein stn1
B: Protein ten1


Theoretical massNumber of molelcules
Total (without water)30,5282
Polymers30,5282
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-10.2 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.871, 93.871, 56.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-101-

HOH

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Components

#1: Protein Protein stn1


Mass: 18755.656 Da / Num. of mol.: 1 / Fragment: N-terminal fragment: UNP residues 2-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: stn1, SPBC409.12c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q0E7J7
#2: Protein Protein ten1


Mass: 11772.649 Da / Num. of mol.: 1 / Fragment: UNP residues 2-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: ten1, SPCC1393.14 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0C5Y7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 12% PEG 4000, 12% Isopropanol, 0.1 M Sodium citrate pH 5.6, 5 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. all: 35289 / Num. obs: 30813 / % possible obs: 88 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 42.3

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→50 Å
RfactorNum. reflection% reflection
Rfree0.2442 2931 -
Rwork0.2257 --
obs0.2257 29369 95.3 %
all-30468 -
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 0 191 2142

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