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- PDB-4xyh: Wild-type full length Mis16 in Schizosaccharomyces japonicus -

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Basic information

Entry
Database: PDB / ID: 4xyh
TitleWild-type full length Mis16 in Schizosaccharomyces japonicus
ComponentsKinetochore 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 / histone binding / chromatin remodeling / regulation of DNA-templated transcription / 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. / Trp-Asp (WD) repeats profile. ...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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / 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 japonicus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.0Jan 13, 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

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Assembly

Deposited unit
A: Kinetochore protein Mis16


Theoretical massNumber of molelcules
Total (without water)48,4631
Polymers48,4631
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.342, 134.342, 72.133
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium acetate 0.1 M sodium cacodylate 18% PEG 8000

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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: 2.3→34.158 Å / Num. obs: 30905 / % possible obs: 93.36 % / Redundancy: 10.9 % / Rsym value: 0.092 / Net I/σ(I): 34.1
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 3.2 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CFS

3cfs


Resolution: 2.3→34.158 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.22 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1864 6.03 %Random selection
Rwork0.1744 ---
obs0.1765 30905 93.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→34.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 0 144 3126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083054
X-RAY DIFFRACTIONf_angle_d1.1344167
X-RAY DIFFRACTIONf_dihedral_angle_d14.7381089
X-RAY DIFFRACTIONf_chiral_restr0.046468
X-RAY DIFFRACTIONf_plane_restr0.005541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.36230.29171170.25791841X-RAY DIFFRACTION78
2.3623-2.43180.31371250.24221975X-RAY DIFFRACTION83
2.4318-2.51030.28641380.23282088X-RAY DIFFRACTION88
2.5103-2.60.24451370.20912119X-RAY DIFFRACTION90
2.6-2.7040.2661410.20292190X-RAY DIFFRACTION92
2.704-2.82710.25631430.19142232X-RAY DIFFRACTION94
2.8271-2.9760.25081400.19782293X-RAY DIFFRACTION96
2.976-3.16240.21371470.19042326X-RAY DIFFRACTION97
3.1624-3.40630.21611540.17012348X-RAY DIFFRACTION99
3.4063-3.74870.19381550.14982392X-RAY DIFFRACTION100
3.7487-4.29030.16551560.1452379X-RAY DIFFRACTION99
4.2903-5.40190.13091550.12512412X-RAY DIFFRACTION100
5.4019-34.16130.19231560.17252446X-RAY DIFFRACTION99

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