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- PDB-1pl5: Crystal Structure Analysis of the Sir4p C-terminal Coiled Coil -

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Basic information

Entry
Database: PDB / ID: 1pl5
TitleCrystal Structure Analysis of the Sir4p C-terminal Coiled Coil
ComponentsRegulatory protein SIR4
KeywordsDNA binding protein/Transcription / parallel coiled coil homodimer / DNA binding protein-Transcription COMPLEX
Function / homology
Function and homology information


establishment of protein-containing complex localization to telomere / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / positive regulation of heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin formation / double-strand break repair via nonhomologous end joining / double-stranded DNA binding ...establishment of protein-containing complex localization to telomere / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / positive regulation of heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin formation / double-strand break repair via nonhomologous end joining / double-stranded DNA binding / chromosome, telomeric region / molecular adaptor activity
Similarity search - Function
Single helix bin / Sir4, SID domain / Sir4 SID domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein SIR4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.5 Å
AuthorsMurphy, G.A. / Spedale, E.J. / Powell, S.T. / Pillus, L. / Schultz, S.C. / Chen, L.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Sir4 C-terminal coiled coil is required for telomeric and mating type silencing in Saccharomyces cerevisiae.
Authors: Murphy, G.A. / Spedale, E.J. / Powell, S.T. / Pillus, L. / Schultz, S.C. / Chen, L.
History
DepositionJun 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

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Assembly

Deposited unit
A: Regulatory protein SIR4
S: Regulatory protein SIR4


Theoretical massNumber of molelcules
Total (without water)31,9182
Polymers31,9182
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-37 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.884, 108.884, 75.342
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Regulatory protein SIR4 / Silent information regulator 4


Mass: 15958.884 Da / Num. of mol.: 2 / Fragment: RESIDUES 1217-1358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIR4 / Plasmid: pKKT7E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P11978
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 4.04 Å3/Da / Density % sol: 69.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: calcium chloride, sodium chloride, Tris, ethylene glycol, sodium azide, dithiothreitol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→26.15 Å / Num. all: 29662 / Num. obs: 28687 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.073 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.17 Å / Mean I/σ(I) obs: 0.16 / Num. unique all: 2957 / Rsym value: 0.61 / % possible all: 94.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SIR / Resolution: 2.5→26.15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.288 1684 random
Rwork0.261 --
obs0.261 17291 -
all-19380 -
Displacement parametersBiso mean: 46.87 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 0 40 1211
LS refinement shellResolution: 2.5→2.53 Å

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