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Yorodumi- PDB-4iqy: Crystal structure of the human protein-proximal ADP-ribosyl-hydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iqy | ||||||
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Title | Crystal structure of the human protein-proximal ADP-ribosyl-hydrolase MacroD2 | ||||||
Components | O-acetyl-ADP-ribose deacetylase MACROD2 | ||||||
Keywords | HYDROLASE / macrodomain / ADP-ribose binding / ADP-ribosylation / nuclear/cytoplasmic | ||||||
Function / homology | Function and homology information ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / peptidyl-glutamate ADP-deribosylation / purine nucleoside metabolic process / O-acetyl-ADP-ribose deacetylase activity / deacetylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to bacterium ...ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / peptidyl-glutamate ADP-deribosylation / purine nucleoside metabolic process / O-acetyl-ADP-ribose deacetylase activity / deacetylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to bacterium / brain development / DNA damage response / nucleolus / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Jankevicius, G. / Hassler, M. / Golia, B. / Rybin, V. / Zacharias, M. / Timinszky, G. / Ladurner, A.G. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: A family of macrodomain proteins reverses cellular mono-ADP-ribosylation. Authors: Jankevicius, G. / Hassler, M. / Golia, B. / Rybin, V. / Zacharias, M. / Timinszky, G. / Ladurner, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iqy.cif.gz | 212.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iqy.ent.gz | 167.4 KB | Display | PDB format |
PDBx/mmJSON format | 4iqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iqy_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4iqy_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4iqy_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 4iqy_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/4iqy ftp://data.pdbj.org/pub/pdb/validation_reports/iq/4iqy | HTTPS FTP |
-Related structure data
Related structure data | 2x47S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27070.188 Da / Num. of mol.: 2 / Fragment: macrodomain (UNP residues 7-243) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MACROD2, C20orf133 / Plasmid: pET-MCN 6HisTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS References: UniProt: A1Z1Q3, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% PEG3350, 0.1M HEPES, 0.1M MgFormate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97633 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2010 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97633 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→46.78 Å / Num. all: 80145 / Num. obs: 72823 / % possible obs: 90.86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.47→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2X47 Resolution: 1.55→46.783 Å / SU ML: 0.14 / Isotropic thermal model: anisotropic / σ(F): 0.01 / Phase error: 19.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→46.783 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.8389 Å / Origin y: 6.3717 Å / Origin z: 19.0935 Å
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Refinement TLS group | Selection details: all |