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- PDB-6tx1: HPF1 from Nematostella vectensis -

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Basic information

Entry
Database: PDB / ID: 6tx1
TitleHPF1 from Nematostella vectensis
ComponentsPredicted protein
KeywordsPROTEIN BINDING / PARP1 / PARP2 / ADP-ribosylation / serine ADP-ribosylation / adaptor
Function / homologyHistone PARylation factor 1 / Histone PARylation factor 1 / poly-ADP-D-ribose binding / chromosome / histone binding / DNA damage response / nucleus / Histone PARylation factor 1
Function and homology information
Biological speciesNematostella vectensis (starlet sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.091 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: Predicted protein
B: Predicted protein


Theoretical massNumber of molelcules
Total (without water)76,5352
Polymers76,5352
Non-polymers00
Water5,386299
1
A: Predicted protein


Theoretical massNumber of molelcules
Total (without water)38,2681
Polymers38,2681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Predicted protein


Theoretical massNumber of molelcules
Total (without water)38,2681
Polymers38,2681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.165, 89.165, 223.002
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Predicted protein


Mass: 38267.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nematostella vectensis (starlet sea anemone)
Gene: v1g201271 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A7RS11
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium malonate dibasic monohydrate, 20% v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9199 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 2.09→72.97 Å / Num. obs: 41180 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.137 / Net I/σ(I): 8.1
Reflection shellResolution: 2.09→2.17 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 37974 / CC1/2: 0.7 / Rrim(I) all: 1.74 / % possible all: 99.8

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Processing

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

Resolution: 2.091→72.968 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.85
RfactorNum. reflection% reflection
Rfree0.2708 1956 5 %
Rwork0.205 --
obs0.2079 39121 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.21 Å2 / Biso mean: 49.984 Å2 / Biso min: 26.5 Å2
Refinement stepCycle: final / Resolution: 2.091→72.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 0 299 4996
Biso mean---47.87 -
Num. residues----588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.091-2.14280.36261310.31842686
2.1428-2.20070.34871640.29042602
2.2007-2.26550.31741510.27372665
2.2655-2.33860.29121160.2592669
2.3386-2.42220.30171510.25722643
2.4222-2.51920.38821370.27462636
2.5192-2.63390.38231900.26712597
2.6339-2.77270.32351840.25212641
2.7727-2.94650.29911420.23132627
2.9465-3.1740.36941200.23912690
3.174-3.49340.28111230.21192667
3.4934-3.99880.2218990.1872692
3.9988-5.03790.20821370.16012662
5.0379-72.9680.20161110.15982688

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