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- PDB-6f0f: Crystal structure ASF1-ip2_s -

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Basic information

Entry
Database: PDB / ID: 6f0f
TitleCrystal structure ASF1-ip2_s
Components
  • Histone chaperone ASF1A
  • ip2_s
KeywordsCHAPERONE / protein-peptide complexe
Function / homology
Function and homology information


muscle cell differentiation / histone chaperone activity / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / osteoblast differentiation / nucleosome assembly / site of double-strand break / histone binding ...muscle cell differentiation / histone chaperone activity / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / osteoblast differentiation / nucleosome assembly / site of double-strand break / histone binding / DNA repair / chromatin binding / chromatin / protein-containing complex / nucleoplasm / nucleus
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGaubert, A. / Guichard, B. / Murciano, B. / Le Du, M.H. / Ochsenbein, F. / Guerois, R. / Andreani, J.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyBREAKABOUND France
French National Research AgencyCHAPINHIB France
French National Research AgencyFRISBI France
CitationJournal: Cell Chem Biol / Year: 2019
Title: Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.
Authors: Bakail, M. / Gaubert, A. / Andreani, J. / Moal, G. / Pinna, G. / Boyarchuk, E. / Gaillard, M.C. / Courbeyrette, R. / Mann, C. / Thuret, J.Y. / Guichard, B. / Murciano, B. / Richet, N. / ...Authors: Bakail, M. / Gaubert, A. / Andreani, J. / Moal, G. / Pinna, G. / Boyarchuk, E. / Gaillard, M.C. / Courbeyrette, R. / Mann, C. / Thuret, J.Y. / Guichard, B. / Murciano, B. / Richet, N. / Poitou, A. / Frederic, C. / Le Du, M.H. / Agez, M. / Roelants, C. / Gurard-Levin, Z.A. / Almouzni, G. / Cherradi, N. / Guerois, R. / Ochsenbein, F.
History
DepositionNov 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Histone chaperone ASF1A
B: ip2_s


Theoretical massNumber of molelcules
Total (without water)20,8912
Polymers20,8912
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-5 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.410, 61.410, 220.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-280-

HOH

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Components

#1: Protein Histone chaperone ASF1A / Anti-silencing function protein 1 homolog A / hAsf1a / CCG1-interacting factor A / hCIA


Mass: 17927.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, CGI-98, HSPC146 / Plasmid: pETM30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y294
#2: Protein/peptide ip2_s


Mass: 2963.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 5.06 Å3/Da / Density % sol: 75.67 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: Tris-HCl 0.1M pH7.5, PEG8000 5%

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30.93 Å / Num. obs: 28132 / % possible obs: 100 % / Redundancy: 6.4 % / Net I/σ(I): 24.2
Reflection shellResolution: 2→2.12 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2io5

2io5


Resolution: 2→30.93 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.388 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1481 5 %RANDOM
Rwork0.1864 ---
obs0.1884 28132 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.55 Å2 / Biso mean: 43.094 Å2 / Biso min: 25.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2--1.81 Å20 Å2
3----3.62 Å2
Refinement stepCycle: final / Resolution: 2→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 0 343 1787
Biso mean---57.64 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221497
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9552043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5075184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68624.41677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41415233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3351511
X-RAY DIFFRACTIONr_chiral_restr0.1360.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021177
X-RAY DIFFRACTIONr_nbd_refined0.210.2674
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2993
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.224
LS refinement shellResolution: 1.999→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 105 -
Rwork0.264 1992 -
all-2097 -
obs--100 %

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