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- PDB-6m3g: Crystal structure of human HPF1 -

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Basic information

Entry
Database: PDB / ID: 6m3g
TitleCrystal structure of human HPF1
ComponentsHistone PARylation factor 1
KeywordsNUCLEAR PROTEIN / cofactor / ADP-ribosylation / DNA damage response
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / protein ADP-ribosyltransferase-substrate adaptor activity / poly-ADP-D-ribose binding / DNA repair-dependent chromatin remodeling / site of DNA damage / double-strand break repair / histone binding / DNA repair / DNA damage response / chromatin binding ...regulation of protein ADP-ribosylation / protein ADP-ribosyltransferase-substrate adaptor activity / poly-ADP-D-ribose binding / DNA repair-dependent chromatin remodeling / site of DNA damage / double-strand break repair / histone binding / DNA repair / DNA damage response / chromatin binding / chromatin / nucleus
Similarity search - Function
Histone PARylation factor 1 / Histone PARylation factor 1
Similarity search - Domain/homology
Histone PARylation factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsSun, F.H. / Yun, C.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31270769 China
CitationJournal: Nat Commun / Year: 2021
Title: HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones.
Authors: Sun, F.H. / Zhao, P. / Zhang, N. / Kong, L.L. / Wong, C.C.L. / Yun, C.H.
History
DepositionMar 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 PARylation factor 1


Theoretical massNumber of molelcules
Total (without water)39,4951
Polymers39,4951
Non-polymers00
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.981, 89.981, 226.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-459-

HOH

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Components

#1: Protein Histone PARylation factor 1


Mass: 39495.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPF1, C4orf27
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpGUT1 (others)
References: UniProt: Q9NWY4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 300 K / Method: vapor diffusion
Details: 0.1 M Tris-pH 8.1, 0.2 M potassium acetate, 20% w/v Polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 17, 2018
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 49462 / % possible obs: 99.3 % / Redundancy: 9.6 % / Biso Wilson estimate: 21.57 Å2 / Rpim(I) all: 0.017 / Net I/σ(I): 45.2
Reflection shellResolution: 1.57→1.6 Å / Num. unique obs: 2567 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→45.86 Å / SU ML: 0.1801 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.1315 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2048 2492 5.04 %
Rwork0.1882 46970 -
obs0.1891 49462 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.52 Å2
Refinement stepCycle: LAST / Resolution: 1.57→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 0 341 2780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772533
X-RAY DIFFRACTIONf_angle_d0.94173432
X-RAY DIFFRACTIONf_chiral_restr0.0674372
X-RAY DIFFRACTIONf_plane_restr0.0055450
X-RAY DIFFRACTIONf_dihedral_angle_d16.0594944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60.30481320.26322567X-RAY DIFFRACTION98.9
1.6-1.640.28961150.25042617X-RAY DIFFRACTION100
1.64-1.670.29051250.24712585X-RAY DIFFRACTION100
1.67-1.710.28871390.24812554X-RAY DIFFRACTION100
1.71-1.750.23891430.22972566X-RAY DIFFRACTION100
1.75-1.80.26271390.22682618X-RAY DIFFRACTION100
1.8-1.850.27021500.2162563X-RAY DIFFRACTION100
1.85-1.910.25441340.20782618X-RAY DIFFRACTION100
1.91-1.980.24521450.21222564X-RAY DIFFRACTION100
1.98-2.060.25391480.21042578X-RAY DIFFRACTION100
2.06-2.150.23661140.20222615X-RAY DIFFRACTION100
2.15-2.270.22351510.19372606X-RAY DIFFRACTION100
2.27-2.410.21111340.19432621X-RAY DIFFRACTION100
2.41-2.60.20871280.19182624X-RAY DIFFRACTION100
2.6-2.860.19571500.19252607X-RAY DIFFRACTION99.96
2.86-3.270.20151330.18712653X-RAY DIFFRACTION100
3.27-4.120.15911520.15672656X-RAY DIFFRACTION100
4.12-45.860.16911600.1612758X-RAY DIFFRACTION99.79

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