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- PDB-3zco: Crystal structure of S. cerevisiae Sir3 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3zco
TitleCrystal structure of S. cerevisiae Sir3 C-terminal domain
ComponentsREGULATORY PROTEIN SIR3
KeywordsTRANSCRIPTION / WINGED-HELIX LIKE DOMAIN / DIMERIZATION
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 / nuclear origin of replication recognition complex / chromatin silencing complex / mitotic DNA replication checkpoint signaling / silent mating-type cassette heterochromatin formation / DNA replication origin binding / subtelomeric heterochromatin formation / DNA replication initiation ...establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / nuclear origin of replication recognition complex / chromatin silencing complex / mitotic DNA replication checkpoint signaling / silent mating-type cassette heterochromatin formation / DNA replication origin binding / subtelomeric heterochromatin formation / DNA replication initiation / heterochromatin / nucleosome binding / 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
Arc Repressor Mutant, subunit A - #2450 / AAA lid domain / AAA lid domain / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology (BAH) domain / BAH domain profile. / Arc Repressor Mutant, subunit A / P-loop containing nucleoside triphosphate hydrolase ...Arc Repressor Mutant, subunit A - #2450 / AAA lid domain / AAA lid domain / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology (BAH) domain / BAH domain profile. / Arc Repressor Mutant, subunit A / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein SIR3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsOppikofer, M. / Kueng, S. / Keusch, J.J. / Hassler, M. / Ladurner, A.G. / Gut, H. / Gasser, S.M.
CitationJournal: Embo J. / Year: 2013
Title: Dimerization of Sir3 Via its C-Terminal Winged Helix Domain is Essential for Yeast Heterochromatin Formation.
Authors: Oppikofer, M. / Kueng, S. / Keusch, J.J. / Hassler, M. / Ladurner, A.G. / Gut, H. / Gasser, S.M.
History
DepositionNov 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATORY PROTEIN SIR3


Theoretical massNumber of molelcules
Total (without water)15,9171
Polymers15,9171
Non-polymers00
Water00
1
A: REGULATORY PROTEIN SIR3

A: REGULATORY PROTEIN SIR3


Theoretical massNumber of molelcules
Total (without water)31,8332
Polymers31,8332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area1710 Å2
ΔGint-8.3 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.320, 75.320, 55.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein REGULATORY PROTEIN SIR3 / SILENT INFORMATION REGULATOR 3


Mass: 15916.698 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 840-978
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06701

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 30% PEG 4000, 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 5076 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 88.88 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.7
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.7→28.13 Å / Cor.coef. Fo:Fc: 0.9553 / Cor.coef. Fo:Fc free: 0.9172 / SU R Cruickshank DPI: 0.56 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.525 / SU Rfree Blow DPI: 0.307 / SU Rfree Cruickshank DPI: 0.315
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 728 14.34 %RANDOM
Rwork0.2109 ---
obs0.2181 5076 99.98 %-
Displacement parametersBiso mean: 101.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.006 Å20 Å20 Å2
2---1.006 Å20 Å2
3---2.0119 Å2
Refine analyzeLuzzati coordinate error obs: 0.707 Å
Refinement stepCycle: LAST / Resolution: 2.7→28.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1010 0 0 0 1010
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011025HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.341381HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d378SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes24HARMONIC2
X-RAY DIFFRACTIONt_gen_planes139HARMONIC5
X-RAY DIFFRACTIONt_it1025HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion22.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion141SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1213SEMIHARMONIC4
LS refinement shellResolution: 2.7→3.02 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3225 199 13.85 %
Rwork0.2529 1238 -
all0.2622 1437 -
obs--99.98 %
Refinement TLS params.Method: refined / Origin x: -13.8891 Å / Origin y: 16.2468 Å / Origin z: -1.862 Å
111213212223313233
T0.173 Å20.3173 Å20.2816 Å2--0.0948 Å20.1202 Å2---0.194 Å2
L8.2091 °2-1.409 °20.2747 °2-7.0048 °20.882 °2--3.6815 °2
S-0.4793 Å °-0.1451 Å °-0.4713 Å °-0.6907 Å °0.2499 Å °-0.4801 Å °-0.2575 Å °0.1704 Å °0.2294 Å °
Refinement TLS groupSelection details: CHAIN A

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