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- PDB-1e0b: Chromo shadow domain from fission yeast swi6 protein. -

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Basic information

Entry
Database: PDB / ID: 1e0b
TitleChromo shadow domain from fission yeast swi6 protein.
ComponentsSWI6 PROTEIN
KeywordsCHROMATIN-BINDING / CHROMODOMAIN / SHADOW / HETEROCHROMATIN / SWI6 / POMBE
Function / homology
Function and homology information


meiotic centromeric cohesion protection in anaphase I / Factors involved in megakaryocyte development and platelet production / positive regulation of pericentric heterochromatin formation / gene conversion at mating-type locus / mating type switching / mitotic telomere tethering at nuclear periphery / RNA Polymerase I Promoter Escape / mitotic sister chromatid cohesion, centromeric / mating-type region heterochromatin / heterochromatin island ...meiotic centromeric cohesion protection in anaphase I / Factors involved in megakaryocyte development and platelet production / positive regulation of pericentric heterochromatin formation / gene conversion at mating-type locus / mating type switching / mitotic telomere tethering at nuclear periphery / RNA Polymerase I Promoter Escape / mitotic sister chromatid cohesion, centromeric / mating-type region heterochromatin / heterochromatin island / heterochromatin boundary formation / mitotic sister chromatid biorientation / chromosome, subtelomeric region / chromatin-protein adaptor activity / condensed chromosome, centromeric region / silent mating-type cassette heterochromatin formation / heterochromatin / pericentric heterochromatin / methylated histone binding / histone reader activity / chromatin organization / histone binding / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / identical protein binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-1PG / Chromatin-associated protein swi6
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsCowieson, N.P. / Partridge, J.F. / Allshire, R.C. / Mclaughlin, P.J.
CitationJournal: Curr.Biol. / Year: 2000
Title: Dimerisation of Chromo Shadow Domain and Distinctions from the Chromodomain as Revealed by Structural Analysis
Authors: Cowieson, N.P. / Partridge, J.F. / Allshire, R.C. / Mclaughlin, P.J.
History
DepositionMar 16, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SWI6 PROTEIN
B: SWI6 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3943
Polymers16,1422
Non-polymers2521
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.890, 59.890, 91.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.91, -0.408, -0.079), (-0.403, -0.912, 0.068), (-0.1, -0.03, -0.995)
Vector: 16.954, 49.166, 138.407)

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Components

#1: Protein SWI6 PROTEIN


Mass: 8070.922 Da / Num. of mol.: 2 / Fragment: CHROMO SHADOW DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Description: RECOMBINANT PROTEIN OVEREXPRESSED IN ESCHERICHIA COLI.
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40381
#2: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.93 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 20% (W/V) PEG 4000, 0.2M SODIUM ACETATE, 0.1M TRIS HCL PH 8.5, TEMPERATURE 4 DEGREES CENTIGRADE PROTEIN CONCENTRATION 10 MG/ML TIME 3 TO 4 DAYS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
220 %(w/v)PEG40001reservoir
30.2 Msodium acetate1reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorDate: May 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→22.25 Å / Num. obs: 115148 / % possible obs: 99.8 % / Redundancy: 14 % / Rmerge(I) obs: 0.061
Reflection
*PLUS
Num. measured all: 115148

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Processing

Software
NameVersionClassification
CNS0.9refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→22 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 717 4.9 %RANDOM
Rwork0.226 ---
obs0.226 14642 99.8 %-
Displacement parametersBiso mean: 41.6546 Å2
Baniso -1Baniso -2Baniso -3
1--5.007 Å2-0.447 Å20 Å2
2---5.007 Å20 Å2
3---10.013 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 17 111 1119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.029
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_deg2.2823
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.09289
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.41547
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.6546 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.2823
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.09289
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.41547

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