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- PDB-2fl7: S. cerevisiae Sir3 BAH domain -

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Basic information

Entry
Database: PDB / ID: 2fl7
TitleS. cerevisiae Sir3 BAH domain
ComponentsRegulatory protein SIR3
KeywordsTRANSCRIPTION / Sir / ORC / silencing / chromatin
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKeck, J.L. / Hou, Z. / Daner, J.R. / Fox, C.A.
CitationJournal: Protein Sci. / Year: 2006
Title: Structure of the Sir3 protein bromo adjacent homology (BAH) domain from S. cerevisiae at 1.95 A resolution.
Authors: Hou, Z. / Danzer, J.R. / Fox, C.A. / Keck, J.L.
History
DepositionJan 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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


Theoretical massNumber of molelcules
Total (without water)27,5031
Polymers27,5031
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.633, 44.145, 53.723
Angle α, β, γ (deg.)90.00, 96.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-265-

HOH

DetailsSir3 BAH domain is monomeric

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Components

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


Mass: 27503.273 Da / Num. of mol.: 1 / Fragment: BAH domain, residues 1-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIR3, CMT1, MAR2, STE8 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P06701
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M HEPES, pH 6.5, 200 mM sodium chloride, 10% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: BRUKER PROTEUM R / Detector: CCD / Date: Sep 20, 2005
RadiationMonochromator: Montel 200 Multilayered Graded / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→53.3 Å / Num. all: 19003 / Num. obs: 18434 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.9 Å / % possible all: 70.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
PROTEUM PLUS2 (BRUKER)data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.139 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23242 911 5.1 %RANDOM
Rwork0.19859 ---
all0.2 17634 --
obs0.2 17052 94.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.561 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.56 Å2
2--0.38 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 0 117 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221593
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9572154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2195179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.73524.16784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63615287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0481510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021203
X-RAY DIFFRACTIONr_nbd_refined0.2190.2717
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2131
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.216
X-RAY DIFFRACTIONr_mcbond_it1.0061.5941
X-RAY DIFFRACTIONr_mcangle_it1.63321493
X-RAY DIFFRACTIONr_scbond_it2.2973759
X-RAY DIFFRACTIONr_scangle_it3.7834.5661
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 40 -
Rwork0.246 730 -
obs--56.83 %
Refinement TLS params.Method: refined / Origin x: 15.8283 Å / Origin y: 0.8478 Å / Origin z: 9.0561 Å
111213212223313233
T-0.0497 Å20.0045 Å20.018 Å2--0.0371 Å2-0.0018 Å2---0.0217 Å2
L0.7042 °2-0.0127 °20.5023 °2-0.6373 °2-0.088 °2--1.3193 °2
S-0.0117 Å °0.0056 Å °-0.0128 Å °0.0231 Å °-0.0224 Å °0.0101 Å °-0.0555 Å °0.05 Å °0.0342 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 21511 - 218
2X-RAY DIFFRACTION1AB230 - 346

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