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Yorodumi- PDB-5h6n: DNA targeting ADP-ribosyltransferase Pierisin-1, autoinhibitory form -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h6n | ||||||
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Title | DNA targeting ADP-ribosyltransferase Pierisin-1, autoinhibitory form | ||||||
Components | Pierisin-1 | ||||||
Keywords | TRANSFERASE / DNA-targeting ADP-ribosyltransferase | ||||||
Function / homology | Function and homology information 2'-deoxyguanosine DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / apoptotic process / DNA binding Similarity search - Function | ||||||
Biological species | Pieris rapae (cabbage white) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Oda, T. / Hirabayashi, H. / Shikauchi, G. / Takamura, R. / Hiraga, K. / Minami, H. / Hashimoto, H. / Yamamoto, M. / Wakabayashi, K. / Sugimura, T. ...Oda, T. / Hirabayashi, H. / Shikauchi, G. / Takamura, R. / Hiraga, K. / Minami, H. / Hashimoto, H. / Yamamoto, M. / Wakabayashi, K. / Sugimura, T. / Shimizu, T. / Sato, M. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1 Authors: Oda, T. / Hirabayashi, H. / Shikauchi, G. / Takamura, R. / Hiraga, K. / Minami, H. / Hashimoto, H. / Yamamoto, M. / Wakabayashi, K. / Shimizu, T. / Sato, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h6n.cif.gz | 214.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h6n.ent.gz | 171.6 KB | Display | PDB format |
PDBx/mmJSON format | 5h6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h6n_validation.pdf.gz | 454.6 KB | Display | wwPDB validaton report |
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Full document | 5h6n_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 5h6n_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 5h6n_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/5h6n ftp://data.pdbj.org/pub/pdb/validation_reports/h6/5h6n | HTTPS FTP |
-Related structure data
Related structure data | 5h6jC 5h6kC 5h6lC 5h6mC 2cb4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 31456.125 Da / Num. of mol.: 4 / Fragment: UNP residues 1-267 / Mutation: E165Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pieris rapae (cabbage white) / Plasmid: pGEX6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): codon plus RIPL References: UniProt: H3JU00, UniProt: Q9U8Q4*PLUS, Transferases; Glycosyltransferases; Pentosyltransferases #2: 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: 3.06 Å3/Da / Density % sol: 59.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% (v/v) t-butanol and 0.1M Tris-HCl pH8 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 132451 / % possible obs: 95 % / Redundancy: 3.74 % / Net I/σ(I): 19.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CB4 Resolution: 1.8→30.068 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.909 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.354 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→30.068 Å
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Refine LS restraints |
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