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- PDB-1km9: The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1km9 | |||||||||
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Title | The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog) | |||||||||
![]() | RIBONUCLEASE, OOCYTES | |||||||||
![]() | HYDROLASE / RC-RNase | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
![]() | Chern, S.-S. / Musayev, F.N. / Amiraslanov, I.R. / Liao, Y.-D. / Liaw, Y.-C. | |||||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.8 KB | Display | ![]() |
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PDB format | ![]() | 25.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1km8C ![]() 1rcaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, ammonium phosphate, NaOAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 115 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 25, 1998 / 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: 1.96→24.36 Å / Num. all: 8085 / Num. obs: 8085 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.62 % / Biso Wilson estimate: 17.7 Å2 / Limit h max: 20 / Limit h min: 0 / Limit k max: 23 / Limit k min: 0 / Limit l max: 29 / Limit l min: 0 / Observed criterion F max: 599537.23 / Observed criterion F min: 0.89 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 7.06 / Num. unique all: 402 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RCA Resolution: 1.96→24.36 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: 47.953 Å2 / ksol: 0.309465 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.72 Å2 / Biso mean: 29.53 Å2 / Biso min: 14.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→24.36 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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