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- PDB-1nyh: Crystal Structure of the Coiled-coil Dimerization Motif of Sir4 -

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Basic information

Entry
Database: PDB / ID: 1nyh
TitleCrystal Structure of the Coiled-coil Dimerization Motif of Sir4
ComponentsRegulatory protein SIR4
KeywordsTranscription repressor / coiled-coil / Transcription regulation / Repressor
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 / heterochromatin formation / nucleosome binding / 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 / heterochromatin formation / nucleosome binding / 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 / MAD / Resolution: 3.1 Å
AuthorsChang, J.F. / Hall, B.E. / Tanny, J.C. / Moazed, D. / Filman, D. / Ellenberger, T.
CitationJournal: Structure / Year: 2003
Title: Structure of the Coiled-coil Dimerization Motif of Sir4 and Its Interaction With Sir3
Authors: Chang, J.F. / Hall, B.E. / Tanny, J.C. / Moazed, D. / Filman, D. / Ellenberger, T.
History
DepositionFeb 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 SIR4


Theoretical massNumber of molelcules
Total (without water)18,6531
Polymers18,6531
Non-polymers00
Water00
1
A: Regulatory protein SIR4

A: Regulatory protein SIR4


Theoretical massNumber of molelcules
Total (without water)37,3062
Polymers37,3062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area3690 Å2
ΔGint-40 kcal/mol
Surface area11230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)108.640, 108.640, 74.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -y, -x, 1/6+z and a translation of +1 along a, b and c axes.

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Components

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


Mass: 18652.967 Da / Num. of mol.: 1
Fragment: Coiled-coil dimerization domain, residue 1198-1358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIR4 / Plasmid: pGEX6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11978

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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: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, MES, MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
250 mMHEPES1droppH7.5
3350 mM1dropNaCl
45 mMdithiothreitol1drop
51 mMEDTA1drop
6100 mMMES1reservoirpH6.0
7200 mM1reservoirMgCl2
81 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97827, 0.978423, 0.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2001 / Details: toroidal mirror
RadiationMonochromator: Channel-Cut Si(111)Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978271
20.9784231
30.951
ReflectionResolution: 3.1→47.14 Å / Num. all: 5054 / Num. obs: 4796 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 33.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 9.2 / % possible all: 97.2
Reflection
*PLUS
% possible obs: 96.2 % / Num. measured all: 191300
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→47.14 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.833 / SU B: 14.439 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.425 / ESU R Free: 0.345
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.28797 501 10.5 %RANDOM
Rwork0.27074 ---
all0.27254 5054 --
obs0.27254 4290 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.993 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å21.09 Å20 Å2
2--2.18 Å20 Å2
3----3.26 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms592 0 0 0 592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022596
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.985796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.448575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.297
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02422
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2630.2280
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.184 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 44
Rwork0.347 277
Refinement
*PLUS
Rfactor Rfree: 0.288 / Rfactor Rwork: 0.271
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.184

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