+Open data
-Basic information
Entry | Database: PDB / ID: 7or6 | ||||||
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Title | The crystal structure of the domain-swapped dimer of onconase | ||||||
Components | Protein P-30 | ||||||
Keywords | HYDROLASE / Ribonuclease / Onconase / Onconase dimer / 3D domain swapping / antitumor activity | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / endonuclease activity / nucleic acid binding Similarity search - Function | ||||||
Biological species | Lithobates pipiens (northern leopard frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Merlino, A. / Loreto, D. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2021 Title: The crystal structure of the domain-swapped dimer of onconase highlights some catalytic and antitumor activity features of the enzyme. Authors: Gotte, G. / Campagnari, R. / Loreto, D. / Bettin, I. / Calzetti, F. / Menegazzi, M. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7or6.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7or6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7or6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/7or6 ftp://data.pdbj.org/pub/pdb/validation_reports/or/7or6 | HTTPS FTP |
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-Related structure data
Related structure data | 7ordC 1oncS 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: 11973.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lithobates pipiens (northern leopard frog) Production host: Escherichia coli (E. coli) References: UniProt: P22069, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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 % sol: 31.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 0.2 M sodium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→51.72 Å / Num. obs: 10440 / % possible obs: 99.9 % / Redundancy: 12.2 % / CC1/2: 1 / Rrim(I) all: 0.273 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.12→2.15 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10440 / CC1/2: 0.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ONC Resolution: 2.12→51.719 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.327 / SU ML: 0.163 / Cross valid method: FREE R-VALUE / ESU R: 0.384 / ESU R Free: 0.237 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.241 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→51.719 Å
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Refine LS restraints |
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LS refinement shell |
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