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- PDB-3kf8: Crystal structure of C. tropicalis Stn1-ten1 complex -

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Basic information

Entry
Database: PDB / ID: 3kf8
TitleCrystal structure of C. tropicalis Stn1-ten1 complex
Components
  • Protein stn1
  • Protein ten1
KeywordsSTRUCTURAL PROTEIN / OB fold
Function / homology
Function and homology information


CST complex / single-stranded telomeric DNA binding / telomere capping / chromosome, telomeric region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1040 / 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
Uncharacterized protein / CST complex subunit Stn1 N-terminal domain-containing protein
Similarity search - Component
Biological speciesCandida tropicalis MYA-3404 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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
C: Protein stn1
D: Protein ten1


Theoretical massNumber of molelcules
Total (without water)79,5154
Polymers79,5154
Non-polymers00
Water3,153175
1
A: Protein stn1
B: Protein ten1


Theoretical massNumber of molelcules
Total (without water)39,7572
Polymers39,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-10.5 kcal/mol
Surface area17020 Å2
MethodPISA
2
C: Protein stn1
D: Protein ten1


Theoretical massNumber of molelcules
Total (without water)39,7572
Polymers39,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-14.8 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.072, 92.072, 200.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protein stn1


Mass: 26047.814 Da / Num. of mol.: 2 / Fragment: N-terminal fragment: UNP residues 2-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis MYA-3404 (yeast) / Strain: ATCC MYA-3404 / T1 / Gene: CTRG_01841 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C5M7K9
#2: Protein Protein ten1


Mass: 13709.496 Da / Num. of mol.: 2 / Fragment: UNP residues 2-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis MYA-3404 (yeast) / Strain: ATCC MYA-3404 / T1 / Gene: CTRG_00988 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C5M4J8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
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: Apr 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 34781 / Num. obs: 34725 / % possible obs: 99.8 % / Redundancy: 11 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 31.2

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→50 Å
RfactorNum. reflection% reflection
Rfree0.2645 3444 -
Rwork0.228 --
obs0.228 34616 99.9 %
all-34662 -
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5263 0 0 175 5438

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