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Yorodumi- PDB-2gmk: Crystal structure of onconase double mutant with spontaneously-as... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gmk | |||||||||
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Title | Crystal structure of onconase double mutant with spontaneously-assembled (AMP) 4 stack | |||||||||
Components | P-30 protein | |||||||||
Keywords | HYDROLASE / Onconase / P-30 protein / ribonuclease / anti-tumor / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG | |||||||||
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 / Resolution: 1.65 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 | 2gmk.cif.gz | 44.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gmk.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 2gmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/2gmk ftp://data.pdbj.org/pub/pdb/validation_reports/gm/2gmk | HTTPS FTP |
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-Related structure data
Related structure data | 2i5sC 1oncS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 11800.611 Da / Num. of mol.: 1 / Mutation: T89N,E91A 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: Chemical | ChemComp-AMP / #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: 2.12 Å3/Da / Density % sol: 41.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PROTEIN SOLUTION (21.4 MG/ML PROTEIN) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (30.6% MEPEG 2K, 0.050 M AMP, 0.090 M BisTris pH 6.5) Crystals cryo-protected with the well solution ...Details: PROTEIN SOLUTION (21.4 MG/ML PROTEIN) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (30.6% MEPEG 2K, 0.050 M AMP, 0.090 M BisTris pH 6.5) Crystals cryo-protected with the well solution supplemented with 5% ethylene glycol, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
-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 PROTEUM-R / Detector: CCD / Date: Jan 27, 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: 1.65→66.142 Å / Num. obs: 12645 / % possible obs: 99.9 % / Redundancy: 26.59 % / Rmerge(I) obs: 0.0542 / Net I/σ(I): 40.66 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing MR | Rfactor: 0.414 / Cor.coef. Fo:Fc: 0.565
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1onc Resolution: 1.65→40.927 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.159 / SU B: 1.973 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.113 / 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: 19.346 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→40.927 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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