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Yorodumi- PDB-3bcm: Crystal Structure of The Unswapped Form of P19A/L28Q/N67D BS-RNase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bcm | ||||||
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Title | Crystal Structure of The Unswapped Form of P19A/L28Q/N67D BS-RNase | ||||||
Components | Seminal ribonuclease | ||||||
Keywords | HYDROLASE / domain swapping / bovine seminal ribonuclease / non covalent dimer / antitumor activity / Allosteric enzyme / Endonuclease / Nuclease / Secreted | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Merlino, A. / Ercole, C. / Picone, D. / Pizzo, E. / Mazzarella, L. / Sica, F. | ||||||
Citation | 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. #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: Acta Crystallogr.,Sect.D / Year: 1993 Title: Bovine seminal ribonuclease: structure at 1.9 A resolution Authors: Mazzarella, L. / Capasso, S. / Demasi, D. / Di Lorenzo, G. / Mattia, C.A. / Zagari, A. #3: Journal: Biopolymers / Year: 2004 Title: Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer Authors: Merlino, A. / Vitagliano, L. / Sica, F. / Zagari, A. / Mazzarella, L. #4: Journal: Proteins / Year: 2003 Title: The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative Authors: Sica, F. / Di Fiore, A. / Zagari, A. / Mazzarella, L. #5: Journal: J.Mol.Biol. / Year: 1999 Title: A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease Authors: Vitagliano, L. / Adinolfi, S. / Sica, F. / Merlino, A. / Zagari, A. / Mazzarella, L. #6: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bcm.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bcm.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bcm_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 3bcm_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 3bcm_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 3bcm_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/3bcm ftp://data.pdbj.org/pub/pdb/validation_reports/bc/3bcm | HTTPS FTP |
-Related structure data
Related structure data | 3bcoC 3bcpC 1r5dS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13622.559 Da / Num. of mol.: 2 / Mutation: P19A, L28Q, N67D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: SRN / Plasmid: PET-22B(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P00669, EC: 3.1.27.5 #2: Chemical | ChemComp-PO4 / #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: 2.33 Å3/Da / Density % sol: 47.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 30% methyl pentanediol, 50mM TRIS-HCl pH 8.4, 0.1M ammonium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 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: Nov 22, 2004 |
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: 2.25→25 Å / Num. all: 11915 / Num. obs: 11915 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.25→2.32 Å / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 5 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R5D Resolution: 2.25→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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