+Open data
-Basic information
Entry | Database: PDB / ID: 6m3g | ||||||
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Title | Crystal structure of human HPF1 | ||||||
Components | Histone PARylation factor 1 | ||||||
Keywords | NUCLEAR PROTEIN / cofactor / ADP-ribosylation / DNA damage response | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å | ||||||
Authors | Sun, F.H. / Yun, C.H. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m3g.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m3g.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 6m3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m3g_validation.pdf.gz | 420.6 KB | Display | wwPDB validaton report |
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Full document | 6m3g_full_validation.pdf.gz | 423.1 KB | Display | |
Data in XML | 6m3g_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 6m3g_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/6m3g ftp://data.pdbj.org/pub/pdb/validation_reports/m3/6m3g | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.03 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Dec 17, 2018 |
Radiation | Monochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.57→1.6 Å / Num. unique obs: 2567 / CC1/2: 0.78 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→45.86 Å
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Refine LS restraints |
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LS refinement shell |
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