+Open data
-Basic information
Entry | Database: PDB / ID: 1yv6 | |||||||||
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Title | X-ray structure of M23L onconase at 298K | |||||||||
Components | P-30 protein | |||||||||
Keywords | HYDROLASE / small conformational changes / onconase thermal stability / ribonucleases / antitumor action / dynamics | |||||||||
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: 1.78 Å | |||||||||
Authors | Merlino, A. / Mazzarella, L. / Carannante, A. / Di Fiore, A. / Di Donato, A. / Notomista, E. / Sica, F. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 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: Journal: Proteins / Year: 2002 Title: Reversible substrate-induced domain motions in ribonuclease A Authors: Vitagliano, L. / Merlino, A. / Zagari, A. / Mazzarella, L. #2: Journal: Protein Sci. / Year: 2000 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: Journal: Protein Sci. / Year: 1998 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: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yv6.cif.gz | 31.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yv6.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/1yv6 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/1yv6 | HTTPS FTP |
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-Related 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: 11827.611 Da / Num. of mol.: 1 / Mutation: M23L 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: 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-SO4 / |
#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: 1.95 Å3/Da / Density % sol: 36.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: PEG 8000, lithium sulphate , sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.54 Å |
Detector | Type: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Jan 11, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→20 Å / Num. all: 8880 / Num. obs: 8880 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 1.78→1.82 Å / Rmerge(I) obs: 0.189 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.78→20 Å
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