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- PDB-4kul: Crystal structure of N-terminal acetylated yeast Sir3 BAH domain ... -

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Basic information

Entry
Database: PDB / ID: 4kul
TitleCrystal structure of N-terminal acetylated yeast Sir3 BAH domain V83P mutant
ComponentsRegulatory protein SIR3
KeywordsTRANSCRIPTION / BAH domain / silencing / nucleus
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 / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin / heterochromatin formation / double-strand break repair via nonhomologous end joining ...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 / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin / heterochromatin formation / double-strand break repair via nonhomologous end joining / single-stranded DNA binding / double-stranded DNA binding / chromosome, telomeric region / nucleic acid binding / chromatin binding / nucleolus / mitochondrion / identical protein binding
Similarity search - Function
Bromo adjacent homology (BAH) domain / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / SH3 type barrels. / Roll ...Bromo adjacent homology (BAH) domain / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / 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: 2.62 Å
AuthorsYang, D. / Fang, Q. / Wang, M. / Ren, R. / Wang, H. / He, M. / Sun, Y. / Yang, N. / Xu, R.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: N alpha-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain.
Authors: Yang, D. / Fang, Q. / Wang, M. / Ren, R. / Wang, H. / He, M. / Sun, Y. / Yang, N. / Xu, R.M.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)26,7721
Polymers26,7721
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.227, 43.453, 53.636
Angle α, β, γ (deg.)90.00, 97.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 26772.275 Da / Num. of mol.: 1 / Fragment: BAH domain, UNP residues 2-219 / Mutation: V83P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SIR3, CMT1, MAR2, STE8, YLR442C, L9753.10 / Cell (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06701
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 14% 2-propanol, 0.2M CaCl, 0.1M sodium acetate(pH4.6) , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2013 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 6620 / Num. obs: 6570 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.6 / Num. unique all: 656 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FVU

2fvu


Resolution: 2.62→46.72 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.876 / SU B: 14.438 / SU ML: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27742 355 5.4 %RANDOM
Rwork0.21746 ---
obs0.2208 6215 98.52 %-
all-6620 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.087 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-6.08 Å2
2--0.31 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.62→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 0 25 1654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021669
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.021.9562258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1255190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98924.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2691510
X-RAY DIFFRACTIONr_chiral_restr0.0690.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211275
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
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: 2.616→2.684 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 20 -
Rwork0.282 404 -
obs--90.6 %

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