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- PDB-1r5m: Crystal Structure Of The C-Terminal WD40 Domain Of Sif2 -

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Basic information

Entry
Database: PDB / ID: 1r5m
TitleCrystal Structure Of The C-Terminal WD40 Domain Of Sif2
ComponentsSIR4-interacting protein SIF2
KeywordsTRANSCRIPTION / TRANSCRIPTION COREPRESSOR / WD40 REPEAT / BETA PROPELLER
Function / homology
Function and homology information


: / Set3 complex / negative regulation of meiotic nuclear division / HDACs deacetylate histones / Rpd3L-Expanded complex / : / positive regulation of stress-activated MAPK cascade / histone deacetylase complex / transcription corepressor activity / regulation of DNA-templated transcription ...: / Set3 complex / negative regulation of meiotic nuclear division / HDACs deacetylate histones / Rpd3L-Expanded complex / : / positive regulation of stress-activated MAPK cascade / histone deacetylase complex / transcription corepressor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
LisH / : / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...LisH / : / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
SIR4-interacting protein SIF2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCerna, D. / Wilson, D.K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The structure of Sif2p, a WD repeat protein functioning in the SET3 corepressor complex.
Authors: Cerna, D. / Wilson, D.K.
History
DepositionOct 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIR4-interacting protein SIF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6093
Polymers46,4171
Non-polymers1922
Water5,495305
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.100, 107.100, 82.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein SIR4-interacting protein SIF2


Mass: 46416.602 Da / Num. of mol.: 1 / Fragment: C-TERMINAL WD40 DOMAIN (residues 113-535)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIF2 / Plasmid: pTYB2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38262
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Mes, 0.2M ammonium sulfate, 30% PEG ME 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 16, 2002
Details: 58cm long, Pt-coated, fused silica, vertical focusmirror
RadiationMonochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 77807 / Num. obs: 75148 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 0.041 / Net I/σ(I): 26.5
Reflection shellHighest resolution: 1.55 Å / Mean I/σ(I) obs: 3.17 / Rsym value: 0.358 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Used model from a in lab MAD solved structure of C-Sif2

Resolution: 1.55→26.78 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 587253.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3818 5.1 %RANDOM
Rwork0.19 ---
obs0.19 75148 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.311 Å2 / ksol: 0.372536 e/Å3
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.89 Å20 Å2
2--0.72 Å20 Å2
3----1.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.55→26.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 10 305 3042
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 1.55→1.61 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.232 359 5.2 %
Rwork0.218 6585 -
obs--89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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