+Open data
-Basic information
Entry | Database: PDB / ID: 2i5s | |||||||||
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Title | Crystal structure of onconase with bound nucleic acid | |||||||||
Components |
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Keywords | HYDROLASE/DNA / Onconase / P-30 protein / ribonuclease / anti-tumor / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG / HYDROLASE-DNA COMPLEX | |||||||||
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 | Rana pipiens (northern leopard frog) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | |||||||||
Authors | Bae, E. / Lee, J.E. / Raines, R.T. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG) | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural basis for catalysis by onconase. Authors: Lee, J.E. / Bae, E. / Bingman, C.A. / Phillips Jr., G.N. / Raines, R.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i5s.cif.gz | 42.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i5s.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 2i5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i5s_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 2i5s_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 2i5s_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 2i5s_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/2i5s ftp://data.pdbj.org/pub/pdb/validation_reports/i5/2i5s | HTTPS FTP |
-Related structure data
Related structure data | 2gmkC 1oncS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11845.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rana pipiens (northern leopard frog) / Gene: RNP30_RANPI / Plasmid: pET 22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P22069, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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#2: DNA chain | Mass: 1200.829 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 41.186596 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.003 M SINGLE-STRANDED DNA OLIGOMER) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (25% PEG 3350, 0.1 M HEPES PH 7.5) CRYO-PROTECTED WITH WELL SOLUTION ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.003 M SINGLE-STRANDED DNA OLIGOMER) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (25% PEG 3350, 0.1 M HEPES PH 7.5) CRYO-PROTECTED WITH WELL SOLUTION SUPPLEMENTED WITH 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: May 2, 2006 / Details: MONTEL OPTICS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Graded Multilayer / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→64.6145 Å / Num. obs: 9270 / % possible obs: 99.7 % / Redundancy: 9.84 % / Rmerge(I) obs: 0.1249 / Net I/σ(I): 12.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing MR | Rfactor: 0.569 / Cor.coef. Fo:Fc: 0.23
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-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1ONC Resolution: 1.9→32.49 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.165 / SU B: 3.248 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.158 / 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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.602 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.49 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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