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- PDB-6s1l: Structure of fission yeast Mis16 -

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Basic information

Entry
Database: PDB / ID: 6s1l
TitleStructure of fission yeast Mis16
ComponentsHistone acetyltransferase type B subunit 2
KeywordsCELL CYCLE / centromere mitosis WD40 histone chaperone
Function / homology
Function and homology information


HATs acetylate histones / CENP-A recruiting complex / Neddylation / HDACs deacetylate histones / H3-H4 histone complex chaperone activity / CENP-A containing chromatin assembly / chromosome, centromeric region / kinetochore / histone binding / chromatin remodeling ...HATs acetylate histones / CENP-A recruiting complex / Neddylation / HDACs deacetylate histones / H3-H4 histone complex chaperone activity / CENP-A containing chromatin assembly / chromosome, centromeric region / kinetochore / histone binding / chromatin remodeling / nucleus / cytoplasm
Similarity search - Function
Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats ...Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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
Histone acetyltransferase type B subunit 2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLefevre, S. / Korntner-Vetter, M. / Singleton, M.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome TrustFC001155 United Kingdom
Medical Research Council (United Kingdom)FC001155 United Kingdom
Cancer Research UKFC001155 United Kingdom
CitationJournal: Life Sci Alliance / Year: 2019
Title: Subunit interactions and arrangements in the fission yeast Mis16-Mis18-Mis19 complex.
Authors: Korntner-Vetter, M. / Lefevre, S. / Hu, X.W. / George, R. / Singleton, M.R.
History
DepositionJun 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase type B subunit 2


Theoretical massNumber of molelcules
Total (without water)48,4071
Polymers48,4071
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.797, 123.604, 94.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histone acetyltransferase type B subunit 2 / Kinetochore protein mis16


Mass: 48407.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: mis16, hat2, SPCC1672.10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O94244
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na(OAc)2, 0.8 M NaH2PO4, 1.2 M KH2PO4, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 1.94→53.92 Å / Num. obs: 33131 / % possible obs: 99.9 % / Redundancy: 2 % / Net I/σ(I): 8.38
Reflection shellResolution: 1.94→2.009 Å / Num. unique obs: 3286

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CFS

3cfs


Resolution: 1.94→53.292 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.08
RfactorNum. reflection% reflection
Rfree0.2594 1630 4.92 %
Rwork0.2038 --
obs0.2064 33108 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→53.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 0 126 3155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083109
X-RAY DIFFRACTIONf_angle_d0.934247
X-RAY DIFFRACTIONf_dihedral_angle_d3.5511836
X-RAY DIFFRACTIONf_chiral_restr0.066469
X-RAY DIFFRACTIONf_plane_restr0.006554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.99710.32191380.2992588X-RAY DIFFRACTION100
1.9971-2.06160.3411330.27332586X-RAY DIFFRACTION100
2.0616-2.13530.28331380.26532593X-RAY DIFFRACTION100
2.1353-2.22080.31591410.25242568X-RAY DIFFRACTION100
2.2208-2.32180.23041270.22742622X-RAY DIFFRACTION100
2.3218-2.44420.29341260.23082595X-RAY DIFFRACTION100
2.4442-2.59740.27611280.22092621X-RAY DIFFRACTION100
2.5974-2.79790.27431480.22552595X-RAY DIFFRACTION100
2.7979-3.07950.2751590.222600X-RAY DIFFRACTION100
3.0795-3.5250.23821380.18342641X-RAY DIFFRACTION100
3.525-4.44080.22241100.17292699X-RAY DIFFRACTION100
4.4408-53.31250.2521440.18772770X-RAY DIFFRACTION100

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