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Yorodumi- PDB-3u01: Crystal structure of onconase double mutant C30A/C75A at 1.12 A r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u01 | |||||||||
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Title | Crystal structure of onconase double mutant C30A/C75A at 1.12 A resolution | |||||||||
Components | Protein P-30 | |||||||||
Keywords | HYDROLASE / ANTITUMOR PROTEIN / alpha/beta protein / ranpirnase / endonuclease / nuclease | |||||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.12 Å | |||||||||
Authors | Kurpiewska, K. / Torrent, G. / Ribo, M. / Vilanova, M. / Loch, J. / Lewinski, K. | |||||||||
Citation | Journal: Biopolymers / Year: 2014 Title: Investigating the effects of double mutation C30A/C75A on onconase structure: Studies at atomic resolution. Authors: Kurpiewska, K. / Torrent, G. / Ribo, M. / Loch, J.I. / Vilanova, M. / Lewinski, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u01.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u01.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 3u01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/3u01 ftp://data.pdbj.org/pub/pdb/validation_reports/u0/3u01 | HTTPS FTP |
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-Related structure data
Related structure data | 1oncS S: Starting model for refinement |
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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: 11781.519 Da / Num. of mol.: 1 / Mutation: C30A/C75A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rana pipiens (northern leopard frog) / Plasmid: pET22b(+)/pONC(C30A/C75A) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P22069, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters | ||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: 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: 1.84 Å3/Da / Density % sol: 33.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 30% PEG8000, 0.2 M lithium sulfate, 100 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Jan 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→34.757 Å / Num. all: 34245 / Num. obs: 33823 / % possible obs: 97.5 % / Redundancy: 2.9 % / Rsym value: 0.084 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.12→1.15 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.46 / % possible all: 83.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ONC Resolution: 1.12→34.757 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.483 / SU ML: 0.011 / SU R Cruickshank DPI: 0.0479 / Cross valid method: THROUGHOUT / ESU R: 0.007 / ESU R Free: 0.007 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.257 Å2
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Refinement step | Cycle: LAST / Resolution: 1.12→34.757 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.12→1.149 Å / Total num. of bins used: 20
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