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- PDB-6m3h: Crystal structure of mouse HPF1 -

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Basic information

Entry
Database: PDB / ID: 6m3h
TitleCrystal structure of mouse HPF1
ComponentsHistone PARylation factor 1
KeywordsNUCLEAR PROTEIN / cofactor / ADP-ribosylation / DNA damage response
Function / homology
Function and homology information


: / : / regulation of protein ADP-ribosylation / poly-ADP-D-ribose binding / site of DNA damage / double-strand break repair / histone binding / DNA damage response / chromatin binding / chromatin ...: / : / regulation of protein ADP-ribosylation / poly-ADP-D-ribose binding / site of DNA damage / double-strand break repair / histone binding / DNA damage response / chromatin binding / chromatin / zinc ion binding / nucleus
Similarity search - Function
Histone PARylation factor 1 / Histone PARylation factor 1
Similarity search - Domain/homology
Histone PARylation factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 1.1Nov 29, 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: Histone PARylation factor 1


Theoretical massNumber of molelcules
Total (without water)39,3521
Polymers39,3521
Non-polymers00
Water4,936274
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)42.031, 79.895, 106.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Histone PARylation factor 1


Mass: 39352.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hpf1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q8CFE2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 300 K / Method: vapor diffusion
Details: 0.1M Tris-pH8.3, 0.2 M Potassium citrate tribasic monohydrate, 20% w/v PEG 3350,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97849 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 7, 2018
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 39364 / % possible obs: 99.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 21.62 Å2 / Rpim(I) all: 0.023 / Net I/σ(I): 31.1
Reflection shellResolution: 1.71→1.77 Å / Num. unique obs: 2485 / Rpim(I) all: 0.351

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M3G

6m3g


Resolution: 1.71→44.36 Å / SU ML: 0.1648 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 21.0794 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2175 1925 4.89 %
Rwork0.1821 37439 -
obs0.1838 39364 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.28 Å2
Refinement stepCycle: LAST / Resolution: 1.71→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 0 274 2751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652548
X-RAY DIFFRACTIONf_angle_d0.94313443
X-RAY DIFFRACTIONf_chiral_restr0.0636375
X-RAY DIFFRACTIONf_plane_restr0.0049447
X-RAY DIFFRACTIONf_dihedral_angle_d19.4903960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.3221060.26892485X-RAY DIFFRACTION92.3
1.75-1.80.28081340.22962578X-RAY DIFFRACTION97.94
1.8-1.850.22171390.20462651X-RAY DIFFRACTION99.64
1.85-1.910.22221380.19352673X-RAY DIFFRACTION99.54
1.91-1.980.24421250.19052627X-RAY DIFFRACTION99.78
1.98-2.060.18551320.18342656X-RAY DIFFRACTION99.75
2.06-2.150.22811450.18272676X-RAY DIFFRACTION100
2.15-2.270.20971370.18352663X-RAY DIFFRACTION99.96
2.27-2.410.2151410.18492683X-RAY DIFFRACTION100
2.41-2.60.22121400.18572692X-RAY DIFFRACTION100
2.6-2.860.22651520.19042695X-RAY DIFFRACTION100
2.86-3.270.21441440.18542720X-RAY DIFFRACTION100
3.27-4.120.19591510.16212745X-RAY DIFFRACTION100
4.12-44.360.21981410.17162895X-RAY DIFFRACTION99.77

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