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- PDB-1y92: Crystal structure of the P19A/N67D Variant Of Bovine seminal Ribo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y92 | ||||||
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Title | Crystal structure of the P19A/N67D Variant Of Bovine seminal Ribonuclease | ||||||
![]() | Seminal ribonuclease | ||||||
![]() | HYDROLASE / nuclease | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Picone, D. / Di Fiore, A. / Ercole, C. / Franzese, M. / Sica, F. / Tomaselli, S. / Mazzarella, L. | ||||||
![]() | ![]() Title: The Role of the Hinge Loop in Domain Swapping: THE SPECIAL CASE OF BOVINE SEMINAL RIBONUCLEASE. Authors: Picone, D. / Di Fiore, A. / Ercole, C. / Franzese, M. / Sica, F. / Tomaselli, S. / Mazzarella, L. #1: ![]() Title: Bovine seminal ribonuclease: structure at 1.9 resolution Authors: Mazzarella, L. / Capasso, S. / Demasi, D. / Di Lorenzo, G. / Mattia, C.A. / Zagari, A. #2: ![]() 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. #3: ![]() 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. #4: ![]() 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: ![]() 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: ![]() 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. #7: ![]() Title: A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.9 KB | Display | ![]() |
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PDB format | ![]() | 44.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 432.1 KB | Display | ![]() |
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Full document | ![]() | 435 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y94C ![]() 1r5dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13607.587 Da / Num. of mol.: 2 / Mutation: P19A, N67D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000, Tris-HCl, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Dec 18, 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: 2.2→20 Å / Num. obs: 12492 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 5 / Num. unique all: 681 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1R5D Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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