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- PDB-6f0h: Crystal structure ASF1-ip4 -

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Basic information

Entry
Database: PDB / ID: 6f0h
TitleCrystal structure ASF1-ip4
Components
  • Histone chaperone ASF1A
  • ip4
KeywordsCHAPERONE / protein-peptide complexe
Function / homology
Function and homology information


histone chaperone activity / muscle cell differentiation / 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 ...histone chaperone activity / muscle cell differentiation / 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
CITRIC ACID / Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBakail, M. / Richet, N. / Le Du, M.H. / Andreani, J. / Guerois, R. / Ochsenbein, F.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyCHAPINHIB France
French National Research AgencyFRISBI France
French National Research AgencyBIPBIP 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: ip4
C: Histone chaperone ASF1A
D: ip4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,00511
Polymers41,2444
Non-polymers7617
Water6,503361
1
A: Histone chaperone ASF1A
B: ip4
C: Histone chaperone ASF1A
D: ip4
hetero molecules

A: Histone chaperone ASF1A
B: ip4
C: Histone chaperone ASF1A
D: ip4
hetero molecules

A: Histone chaperone ASF1A
B: ip4
C: Histone chaperone ASF1A
D: ip4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,01433
Polymers123,73212
Non-polymers2,28221
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area25940 Å2
ΔGint-229 kcal/mol
Surface area44340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.440, 73.440, 229.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-333-

HOH

21C-387-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, CGI-98, HSPC146 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9Y294
#2: Protein/peptide ip4


Mass: 2694.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: rational designed peptide / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 368 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Citrate 0.1M pH 2.5, LiSO4 0.5M, PEG8000 10%

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 26500 / % possible obs: 99.9 % / Redundancy: 19.9 % / Biso Wilson estimate: 22.23 Å2 / Rmerge(I) obs: 0.0161 / Net I/σ(I): 14.3
Reflection shellResolution: 1.98→2.14 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.0562 / Mean I/σ(I) obs: 6.5 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
MOLREP11.0.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2io5

2io5


Resolution: 1.98→48.86 Å / Cor.coef. Fo:Fc: 0.9307 / Cor.coef. Fo:Fc free: 0.9067 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 1325 5 %RANDOM
Rwork0.1956 ---
obs0.198 26499 99.9 %-
Displacement parametersBiso mean: 26.76 Å2
Baniso -1Baniso -2Baniso -3
1-5.5007 Å20 Å20 Å2
2--5.5007 Å20 Å2
3----11.0014 Å2
Refine analyzeLuzzati coordinate error obs: 0.224 Å
Refinement stepCycle: 1 / Resolution: 1.98→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 45 361 3243
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012953HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14047HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d982SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes434HARMONIC5
X-RAY DIFFRACTIONt_it2953HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion16.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion378SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3708SEMIHARMONIC4
LS refinement shellResolution: 1.98→2.06 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.273 145 4.98 %
Rwork0.2132 2764 -
all0.2163 2909 -

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