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- PDB-6tx2: Human HPF1 -

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Basic information

Entry
Database: PDB / ID: 6tx2
TitleHuman HPF1
ComponentsHistone PARylation factor 1
KeywordsPROTEIN BINDING / PARP1 / PARP2 / ADP-ribosylation / serine ADP-ribosylation / C4orf27
Function / homology
Function and homology information


protein ADP-ribosyltransferase-substrate adaptor activity / regulation of protein ADP-ribosylation / 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 ...protein ADP-ribosyltransferase-substrate adaptor activity / regulation of protein ADP-ribosylation / 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 / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSuskiewicz, M.J. / Ahel, I.
Funding support United Kingdom, European Union, 5items
OrganizationGrant numberCountry
Wellcome Trust101794 United Kingdom
Wellcome Trust210634 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R007195/1 United Kingdom
Cancer Research UKC35050/A22284 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 879-2017European Union
CitationJournal: Nature / Year: 2020
Title: HPF1 completes the PARP active site for DNA damage-induced ADP-ribosylation.
Authors: Suskiewicz, M.J. / Zobel, F. / Ogden, T.E.H. / Fontana, P. / Ariza, A. / Yang, J.C. / Zhu, K. / Bracken, L. / Hawthorne, W.J. / Ahel, D. / Neuhaus, D. / Ahel, I.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 1, 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 PARylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7762
Polymers36,7531
Non-polymers231
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.099, 115.099, 90.388
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Histone PARylation factor 1


Mass: 36753.031 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 BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9NWY4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 33% glycerol ethoxylate, 0.23 M lithium citrate tribasic tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9787 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.09→99.68 Å / Num. obs: 80356 / % possible obs: 99.71 % / Redundancy: 19.66 % / CC1/2: 1 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.5
Reflection shellResolution: 2.09→2.17 Å / Redundancy: 18.68 % / Rmerge(I) obs: 2.67 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7931 / CC1/2: 0.79 / % possible all: 98.94

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXdev_3126refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HPF1 from Nematostella vectensis

Resolution: 2.09→57.55 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.8
RfactorNum. reflection% reflection
Rfree0.2073 1964 4.89 %
Rwork0.1885 --
obs0.1894 40174 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.35 Å2 / Biso mean: 47.3036 Å2 / Biso min: 29.59 Å2
Refinement stepCycle: final / Resolution: 2.09→57.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 1 200 2679
Biso mean--47.62 53 -
Num. residues----304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.09-2.1420.31411600.2995265899
2.142-2.19990.29921370.2837269199
2.1999-2.26470.28771690.262270999
2.2647-2.33780.28311470.2585267799
2.3378-2.42130.26461320.22862729100
2.4213-2.51830.23841590.2232271499
2.5183-2.63290.20621520.20742707100
2.6329-2.77170.2371250.21212736100
2.7717-2.94530.22031270.21142754100
2.9453-3.17270.2271290.21122751100
3.1727-3.4920.23581210.19972764100
3.492-3.99720.17441290.16282748100
3.9972-5.03560.14711320.1472778100
5.0356-57.550.19461450.16282794100

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