[English] 日本語
Yorodumi- PDB-5h6l: DNA targeting ADP-ribosyltransferase Pierisin-1 in complex with b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h6l | ||||||
---|---|---|---|---|---|---|---|
Title | DNA targeting ADP-ribosyltransferase Pierisin-1 in complex with beta-NAD+ | ||||||
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: 2.1 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5h6l.cif.gz | 109.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5h6l.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 5h6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/5h6l ftp://data.pdbj.org/pub/pdb/validation_reports/h6/5h6l | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31232.014 Da / Num. of mol.: 2 / Fragment: UNP residues 1-233 / Mutation: Q165E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pieris rapae (cabbage white) / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS References: UniProt: H3JU00, UniProt: Q9U8Q4*PLUS, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris-HCl pH8.0, 20% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.67 Å / Num. obs: 45134 / % possible obs: 99.6 % / Redundancy: 10.33 % / Net I/σ(I): 13.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→9.999 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.237 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 37.473 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→9.999 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|