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Yorodumi- PDB-3f8g: The X-ray structure of a dimeric variant of human pancreatic ribo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f8g | ||||||
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Title | The X-ray structure of a dimeric variant of human pancreatic ribonuclease with high cytotoxic and antitumor activities | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / antitumor agent / ribonuclease / 3d domain swapping / unswapped dimer / dimers / Endonuclease / Glycoprotein / Nuclease / Secreted | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / Late endosomal microautophagy / Chaperone Mediated Autophagy / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Merlino, A. / Avella, G. / Mazzarella, L. / Sica, F. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant. Authors: Merlino, A. / Avella, G. / Di Gaetano, S. / Arciello, A. / Piccoli, R. / Mazzarella, L. / Sica, F. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Structure and stability of the non-covalent swapped dimer of bovine seminal ribonuclease: an enzyme tailored to evade ribonuclease protein inhibitor. Authors: Sica, F. / Di Fiore, A. / Merlino, A. / Mazzarella, L. #2: Journal: J.Mol.Biol. / Year: 2008 Title: The buried diversity of bovine seminal ribonuclease: shape and cytotoxicity of the swapped non-covalent form of the enzyme. Authors: Merlino, A. / Ercole, C. / Picone, D. / Pizzo, E. / Mazzarella, L. / Sica, F. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: A dimeric mutant of human pancreatic ribonuclease with selective cytotoxicity toward malignant cells. Authors: Piccoli, R. / Di Gaetano, S. / De Lorenzo, C. / Grauso, M. / Monaco, C. / Spalletti-Cernia, D. / Laccetti, P. / Cinatl, J. / Matousek, J. / D'Alessio, G. #4: Journal: Biochem.J. / Year: 2001 Title: Second generation antitumour human RNase: significance of its structural and functional features for the mechanism of antitumour action. Authors: Di Gaetano, S. / D'alessio, G. / Piccoli, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f8g.cif.gz | 65.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f8g.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 3f8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f8g_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 3f8g_full_validation.pdf.gz | 455.7 KB | Display | |
Data in XML | 3f8g_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 3f8g_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/3f8g ftp://data.pdbj.org/pub/pdb/validation_reports/f8/3f8g | HTTPS FTP |
-Related structure data
Related structure data | 1e21S 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: 14114.071 Da / Num. of mol.: 2 / Mutation: Q28L, R31C, R32C, N34K, E111G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE1, RIB1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07998, EC: 3.1.27.5 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: A protein solution of 10mg/ml in 10mM Tris acteate ph 7.0, 300mM NaCl was equilibrated against a solution containing 27% w/v PEG, 0.2 M AS, and 100mM cacodylate buffer ph 6.5, VAPOR ...Details: A protein solution of 10mg/ml in 10mM Tris acteate ph 7.0, 300mM NaCl was equilibrated against a solution containing 27% w/v PEG, 0.2 M AS, and 100mM cacodylate buffer ph 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 14, 2005 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 9128 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.09 / Net I/σ(I): 20 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1E21, the crystal structure of des(1-7)RNase Resolution: 2.6→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→40 Å
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