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- PDB-2fvu: Structure of the yeast Sir3 BAH domain -

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Basic information

Entry
Database: PDB / ID: 2fvu
TitleStructure of the yeast Sir3 BAH domain
ComponentsRegulatory protein SIR3
KeywordsTRANSCRIPTION / mainly beta
Function / homology
Function and homology information


establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / negative regulation of DNA replication / DNA replication origin binding / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin ...establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / negative regulation of DNA replication / DNA replication origin binding / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin / heterochromatin formation / double-strand break repair via nonhomologous end joining / single-stranded DNA binding / double-stranded DNA binding / nucleic acid binding / chromosome, telomeric region / chromatin binding / nucleolus / mitochondrion / identical protein binding
Similarity search - Function
Regulatory protein SIR3, C-terminal domain / Bromo adjacent homology (BAH) domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. ...Regulatory protein SIR3, C-terminal domain / Bromo adjacent homology (BAH) domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / SH3 type barrels. / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Regulatory protein SIR3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, R.M.
CitationJournal: Mol.Cell.Biol. / Year: 2006
Title: Structure and function of the Saccharomyces cerevisiae Sir3 BAH domain.
Authors: Connelly, J.J. / Yuan, P. / Hsu, H.C. / Li, Z. / Xu, R.M. / Sternglanz, R.
History
DepositionJan 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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 ...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: Regulatory protein SIR3
B: Regulatory protein SIR3


Theoretical massNumber of molelcules
Total (without water)52,8102
Polymers52,8102
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-5 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.390, 130.390, 65.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThere are two molecules per asymmetric unit, which may or may not have physiological meanings. The purified protein exits as a monomer in solution.

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Components

#1: Protein Regulatory protein SIR3 / Silent information regulator 3


Mass: 26405.016 Da / Num. of mol.: 2 / Fragment: BAH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIR3 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06701
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 3.75
Details: 4M sodium formate, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 50308 / Num. obs: 47561 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.077
Reflection shellResolution: 1.9→1.97 Å / % possible all: 89.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.308 2069 4.8 %RANDOM
Rwork0.28 ---
all0.28 40923 --
obs0.28 40923 94.9 %-
Solvent computationBsol: 55.636 Å2
Displacement parametersBiso mean: 32.349 Å2
Baniso -1Baniso -2Baniso -3
1--3.617 Å2-5.364 Å20 Å2
2---3.617 Å20 Å2
3---7.233 Å2
Refinement stepCycle: LAST / Resolution: 2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 0 124 3353
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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