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Yorodumi- PDB-7ny6: Crystal structure of the Capsaspora owczarzaki macroH2A macrodomain -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ny6 | |||||||||
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Title | Crystal structure of the Capsaspora owczarzaki macroH2A macrodomain | |||||||||
Components | Histone macroH2A1.1 | |||||||||
Keywords | NUCLEAR PROTEIN / macrodomain / ADP-ribose / NAD+ metabolism / PARP1 | |||||||||
Function / homology | Function and homology information regulation of NAD metabolic process / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Capsaspora owczarzaki | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | |||||||||
Authors | Knobloch, G. / Guberovic, I. / Basquin, J. / Buschbeck, M. / Ladurner, A.G. | |||||||||
Funding support | Spain, European Union, 2items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2021 Title: Evolution of a histone variant involved in compartmental regulation of NAD metabolism. Authors: Guberovic, I. / Hurtado-Bages, S. / Rivera-Casas, C. / Knobloch, G. / Malinverni, R. / Valero, V. / Leger, M.M. / Garcia, J. / Basquin, J. / Gomez de Cedron, M. / Frigole-Vivas, M. / Cheema, ...Authors: Guberovic, I. / Hurtado-Bages, S. / Rivera-Casas, C. / Knobloch, G. / Malinverni, R. / Valero, V. / Leger, M.M. / Garcia, J. / Basquin, J. / Gomez de Cedron, M. / Frigole-Vivas, M. / Cheema, M.S. / Perez, A. / Ausio, J. / Ramirez de Molina, A. / Salvatella, X. / Ruiz-Trillo, I. / Eirin-Lopez, J.M. / Ladurner, A.G. / Buschbeck, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ny6.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ny6.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ny6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/7ny6 ftp://data.pdbj.org/pub/pdb/validation_reports/ny/7ny6 | HTTPS FTP |
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-Related structure data
Related structure data | 7ny7C 3iidS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23006.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Capsaspora owczarzaki (strain ATCC 30864) (eukaryote) Strain: ATCC 30864 / Gene: CAOG_004778 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D2UG83 | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.76 Å3/Da / Density % sol: 30.17 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris (pH 5.5) 25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.338→41 Å / Num. obs: 32600 / % possible obs: 90.05 % / Redundancy: 5.9 % / Biso Wilson estimate: 16.32 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.074 / Net I/σ(I): 13.69 |
Reflection shell | Resolution: 1.338→1.386 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 1630 / CC1/2: 0.62 / Rrim(I) all: 0.74 / % possible all: 45.63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IID Resolution: 1.34→41 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→41 Å
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Refine LS restraints |
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LS refinement shell |
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