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Yorodumi- PDB-1km8: The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1km8 | |||||||||
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Title | The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog) | |||||||||
Components | RIBONUCLEASE, OOCYTES | |||||||||
Keywords | HYDROLASE / RC-RNase | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / carbohydrate binding / angiogenesis / endonuclease activity / defense response to Gram-negative bacterium / nucleic acid binding / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | |||||||||
Biological species | Rana catesbeiana (American bullfrog) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Chern, S.-S. / Musayev, F.N. / Amiraslanov, I.R. / Liao, Y.-D. / Liaw, Y.-C. | |||||||||
Citation | Journal: To be Published Title: The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog) Authors: Chern, S.-S. / Musayev, F.N. / Amiraslanov, I.R. / Liao, Y.-D. / Liaw, Y.-C. #1: Journal: J.Biomol.NMR / Year: 1996 Title: The Secondary Structure of a Pyrimidine-Guanine Sequence-Specific Ribonuclease Possessing Cytotoxic Activity From the Oocytes of Rana Catesbeiana Authors: Chen, C. / Hom, K. / Huang, R.F. / Chou, P.J. / Liao, Y.D. / Huang, T. #2: Journal: J.Mol.Biol. / Year: 1998 Title: The Solution Structure of a Cytotoxic Ribonuclease From the Oocytes of Rana catesbeiana (bullfrog) Authors: Chang, C.F. / Chen, C. / Chen, Y.C. / Hom, K. / F Huang, R. / Huang, T.H. #3: Journal: J.Biol.Chem. / Year: 1998 Title: The Rana catesbeiana rcr gene encoding a cytotoxic ribonuclease : Tissue distribution, cloning, purification, cytotoxicity, and active residues for RNase activity Authors: Huang, H.C. / Wang, S.C. / Leu, Y.J. / Lu, S.C. / Liao, Y.D. #4: Journal: Nucleic Acids Res. / Year: 2000 Title: Purification and cloning of cytotoxic ribonucleases from Rana catesbeiana (bullfrog) Authors: Liao, Y.D. / Huang, H.C. / Leu, Y.J. / Wei, C.W. / C Tang, P. / Wang, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1km8.cif.gz | 37.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1km8.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 1km8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1km8_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 1km8_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 1km8_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1km8_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/1km8 ftp://data.pdbj.org/pub/pdb/validation_reports/km/1km8 | HTTPS FTP |
-Related structure data
Related structure data | 1km9C 1oncS C: citing same article (ref.) 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: 12459.343 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: oocytes / Source: (natural) Rana catesbeiana (American bullfrog) / References: UniProt: P11916, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-PO4 / |
#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: 1.89 Å3/Da / Density % sol: 34.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Ammonium phosphate, Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 115 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 26, 1997 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25.14 Å / Num. all: 7650 / Num. obs: 7650 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.24 % / Biso Wilson estimate: 12.9 Å2 / Limit h max: 15 / Limit h min: 0 / Limit k max: 23 / Limit k min: 0 / Limit l max: 35 / Limit l min: 0 / Observed criterion F max: 528021.47 / Observed criterion F min: 0.95 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 10.89 / Num. unique all: 324 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ONC Resolution: 1.9→25.14 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 43.7407 Å2 / ksol: 0.334872 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.31 Å2 / Biso mean: 22.13 Å2 / Biso min: 10.46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→25.14 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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