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Open data
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Basic information
Entry | Database: PDB / ID: 1yv7 | |||||||||
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Title | X-ray structure of (C87S,des103-104) onconase | |||||||||
![]() | P-30 protein | |||||||||
![]() | HYDROLASE / small conformational changes / onconase thermal stability / ribonucleases / antitumor action / dynamics | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
![]() | Merlino, A. / Mazzarella, L. / Carannante, A. / Di Fiore, A. / Di Donato, A. / Notomista, E. / Sica, F. | |||||||||
![]() | ![]() Title: The Importance of Dynamic Effects on the Enzyme Activity: X-RAY STRUCTURE AND MOLECULAR DYNAMICS OF ONCONASE MUTANTS Authors: Merlino, A. / Mazzarella, L. / Carannante, A. / Di Fiore, A. / Di Donato, A. / Notomista, E. / Sica, F. #1: ![]() Title: Reversible substrate-induced domain motions in ribonuclease A Authors: Vitagliano, L. / Merlino, A. / Zagari, A. / Mazzarella, L. #2: ![]() Title: Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine Authors: Vitagliano, L. / Merlino, A. / Zagari, A. / Mazzarella, L. #3: ![]() Title: Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine Authors: Vitagliano, L. / Adinolfi, S. / Riccio, A. / Sica, F. / Zagari, A. / Mazzarella, L. #4: ![]() Title: Atomic resolution structures of ribonuclease A at six pH values Authors: Berisio, R. / Sica, F. / Lamzin, V.S. / Wilson, K.S. / Zagari, A. / Mazzarella, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.7 KB | Display | ![]() |
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PDB format | ![]() | 25.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.3 KB | Display | ![]() |
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Full document | ![]() | 444.9 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yv4C ![]() 1yv6C ![]() 1oncS 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: 11639.362 Da / Num. of mol.: 1 / Fragment: residues 1-102 / Mutation: C87S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rana pipiens (northern leopard frog) / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: P22069, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: PEG 8000, lithium sulphate, sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Mar 19, 2003 |
Radiation | 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→20 Å / Num. all: 7322 / Num. obs: 7322 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.177 / % possible all: 92.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ONC Resolution: 1.9→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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