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- PDB-7ord: The crystal structure of the domain-swapped dimer of onconase (2) -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ord | ||||||
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Title | The crystal structure of the domain-swapped dimer of onconase (2) | ||||||
![]() | Protein P-30 | ||||||
![]() | HYDROLASE / Ribonuclease / Onconase / Onconase dimer / 3D domain swapping / antitumor activity | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
![]() | Merlino, A. / Loreto, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 460.3 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7or6C ![]() 1oncS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: ![]() ![]() References: UniProt: P22069, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | ChemComp-ACT / | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl pH 8.5 25% PEG 3350 0.2 M Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→58.59 Å / Num. obs: 11313 / % possible obs: 97.4 % / Redundancy: 5.9 % / CC1/2: 1 / Rrim(I) all: 0.124 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.14→2.18 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 11313 / CC1/2: 0.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ONC Resolution: 2.14→58.59 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.645 / SU ML: 0.187 / Cross valid method: FREE R-VALUE / ESU R: 0.345 / ESU R Free: 0.245 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: 29.169 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→58.59 Å
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Refine LS restraints |
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LS refinement shell |
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