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- PDB-4xyi: Mis16 with H4 peptide -

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Basic information

Entry
Database: PDB / ID: 4xyi
TitleMis16 with H4 peptide
Components
  • Histone H4
  • Kinetochore protein Mis16
KeywordsCHAPERONE / Centromere / CENP-A / kinetochore / Mis18 complex / histone
Function / homology
Function and homology information


CENP-A recruiting complex / Rpd3L complex / Rpd3L-Expanded complex / CENP-A containing chromatin assembly / kinetochore / structural constituent of chromatin / nucleosome / nucleosome assembly / histone binding / chromatin remodeling ...CENP-A recruiting complex / Rpd3L complex / Rpd3L-Expanded complex / CENP-A containing chromatin assembly / kinetochore / structural constituent of chromatin / nucleosome / nucleosome assembly / histone binding / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / 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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 ...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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone H4 / Kinetochore protein Mis16
Similarity search - Component
Biological speciesSchizosaccharomyces japonicus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAn, S. / Kim, H. / Cho, U.-S.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Mis16 Independently Recognizes Histone H4 and the CENP-ACnp1-Specific Chaperone Scm3sp.
Authors: An, S. / Kim, H. / Cho, U.S.
History
DepositionFeb 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_radiation / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_radiation.pdbx_diffrn_protocol / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Kinetochore protein Mis16
B: Histone H4


Theoretical massNumber of molelcules
Total (without water)59,8832
Polymers59,8832
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-4 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.226, 136.226, 65.536
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 Kinetochore protein Mis16


Mass: 48462.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces japonicus (strain yFS275 / FY16936) (yeast)
Strain: yFS275 / FY16936 / Gene: SJAG_03867 / Plasmid: pFastBac HTb / Cell line (production host): Hi-5 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: B6K598
#2: Protein Histone H4


Mass: 11420.441 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Schizosaccharomyces japonicus (strain yFS275 / FY16936) (yeast)
References: UniProt: B6JV96

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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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5 M disodium phosphate 0.5 M dipotassium phosphate 0.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 14170 / % possible obs: 99.52 % / Redundancy: 8.8 % / Rsym value: 0.11 / Net I/σ(I): 15.7
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 2.5 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XYH

4xyh


Resolution: 3→39.325 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1426 10.06 %Random selection
Rwork0.1997 ---
obs0.2028 14170 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→39.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 0 0 3079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113151
X-RAY DIFFRACTIONf_angle_d1.4614292
X-RAY DIFFRACTIONf_dihedral_angle_d18.3081132
X-RAY DIFFRACTIONf_chiral_restr0.061480
X-RAY DIFFRACTIONf_plane_restr0.006557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.09510.39431320.33611261X-RAY DIFFRACTION98
3.0951-3.21890.36981420.28161236X-RAY DIFFRACTION99
3.2189-3.36540.31731340.25071273X-RAY DIFFRACTION100
3.3654-3.54270.22881430.21181253X-RAY DIFFRACTION100
3.5427-3.76450.21541470.19021279X-RAY DIFFRACTION100
3.7645-4.05490.26271440.19471269X-RAY DIFFRACTION100
4.0549-4.46240.1891410.16081282X-RAY DIFFRACTION100
4.4624-5.10690.15531420.14371286X-RAY DIFFRACTION100
5.1069-6.42970.23031460.18951287X-RAY DIFFRACTION100
6.4297-39.32840.21031550.20331318X-RAY DIFFRACTION100

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