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- PDB-6rrv: Crystal structure of the Sir4 H-BRCT domain -

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Basic information

Entry
Database: PDB / ID: 6rrv
TitleCrystal structure of the Sir4 H-BRCT domain
ComponentsRegulatory protein SIR4
KeywordsNUCLEAR PROTEIN / Heterochromatin
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
Sir4, SID domain / Sir4 SID domain
Similarity search - Domain/homology
BROMIDE ION / Regulatory protein SIR4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsDeshpande, I. / Keusch, J.J. / Challa, K. / Iesmantavicius, V. / Gasser, S.M. / Gut, H.
CitationJournal: Embo J. / Year: 2019
Title: The Sir4 H-BRCT domain interacts with phospho-proteins to sequester and repress yeast heterochromatin.
Authors: Deshpande, I. / Keusch, J.J. / Challa, K. / Iesmantavicius, V. / Gasser, S.M. / Gut, H.
History
DepositionMay 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 15, 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: Regulatory protein SIR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9873
Polymers14,8721
Non-polymers1152
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-5 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.660, 38.130, 48.620
Angle α, β, γ (deg.)90.00, 118.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1075-

ARG

21A-1075-

ARG

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Components

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


Mass: 14871.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fragment (residues 961-1085)
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIR4, ASD1, STE9, UTH2, YDR227W, YD9934.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: P11978
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.92 Å3/Da / Density % sol: 35.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 35% PEG 2000 MME 150 mM potassium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.1→42.9 Å / Num. obs: 43703 / % possible obs: 95.2 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rsym value: 0.034 / Net I/σ(I): 20.8
Reflection shellResolution: 1.1→1.13 Å / Mean I/σ(I) obs: 7 / Num. unique obs: 2598 / CC1/2: 0.98 / Rsym value: 0.128

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→42.892 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 12.32
RfactorNum. reflection% reflection
Rfree0.1417 2206 5.05 %
Rwork0.1172 --
obs0.1184 43698 95.44 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 1.1→42.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 2 213 1261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011209
X-RAY DIFFRACTIONf_angle_d1.2491646
X-RAY DIFFRACTIONf_dihedral_angle_d16.227486
X-RAY DIFFRACTIONf_chiral_restr0.084171
X-RAY DIFFRACTIONf_plane_restr0.006222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.12390.15631000.11232043X-RAY DIFFRACTION76
1.1239-1.150.13121150.10292420X-RAY DIFFRACTION89
1.15-1.17880.13261340.09652518X-RAY DIFFRACTION93
1.1788-1.21070.14341260.10282536X-RAY DIFFRACTION93
1.2107-1.24630.13761210.1032565X-RAY DIFFRACTION94
1.2463-1.28650.13341510.09922584X-RAY DIFFRACTION96
1.2865-1.33250.15081520.10062558X-RAY DIFFRACTION96
1.3325-1.38590.13921460.09822641X-RAY DIFFRACTION97
1.3859-1.44890.12911430.09382656X-RAY DIFFRACTION98
1.4489-1.52530.12071440.09092708X-RAY DIFFRACTION99
1.5253-1.62090.11981440.09292659X-RAY DIFFRACTION99
1.6209-1.7460.12651440.09592703X-RAY DIFFRACTION99
1.746-1.92180.12891540.10862695X-RAY DIFFRACTION99
1.9218-2.19980.13991370.1112716X-RAY DIFFRACTION99
2.1998-2.77150.13531600.12752682X-RAY DIFFRACTION99
2.7715-42.92440.17151350.14832808X-RAY DIFFRACTION99

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