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- PDB-11bg: A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING IN BO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 11bg | ||||||
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Title | A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING IN BOVINE SEMINAL RIBONUCLEASE | ||||||
![]() | PROTEIN (BOVINE SEMINAL RIBONUCLEASE) | ||||||
![]() | HYDROLASE / PHOSPHORIC DIESTER / RNA | ||||||
Function / homology | ![]() : / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / metabolic process / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Vitagliano, L. / Adinolfi, S. / Sica, F. / Merlino, A. / Zagari, A. / Mazzarella, L. | ||||||
![]() | ![]() 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. #1: ![]() Title: Crystallization of Multiple Forms of Bovine Seminal Ribonuclease in the Liganded and Unliganded State Authors: Sica, F. / Adinolfi, S. / Berisio, R. / De Lorenzo, C. / Mazzarella, L. / Piccoli, R. / Vitagliano, L. / Zagari, A. #2: ![]() 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. #3: ![]() Title: Cosolute Effect on Crystallization of Two Dinucleotide Complexes of Bovine Seminal Ribonuclease from Concentrated Salt Solutions Authors: Sica, F. / Adinolfi, S. / Vitagliano, L. / Zagari, A. / Capasso, S. / Mazzarella, L. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: Swapping structural determinants of ribonucleases: an energetic analysis of the hinge peptide 16-22. Authors: Mazzarella, L. / Vitagliano, L. / Zagari, A. #5: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.7 KB | Display | ![]() |
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PDB format | ![]() | 50.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 630.4 KB | Display | ![]() |
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Full document | ![]() | 632.5 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bsrS 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13632.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BOVINE (BOS TAURUS) SEMINAL FLUID / Source: (natural) ![]() ![]() References: UniProt: RNS_BOVIN, UniProt: P00669*PLUS, EC: 3.1.27.5 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-U2G / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.68 % | ||||||||||||||||||||
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Crystal grow | pH: 4.8 / Details: pH 4.8 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: unknown / Details: nucleotide to protein molar ratio of 8:1 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Oct 15, 1996 / Details: MIRRORS |
Radiation | Monochromator: FILTER / 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. obs: 20713 / % possible obs: 96.7 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 1.9→1.93 Å / % possible all: 90.3 |
Reflection | *PLUS Num. measured all: 97315 |
Reflection shell | *PLUS % possible obs: 90 % / Rmerge(I) obs: 0.245 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: 1BSR Resolution: 1.9→12 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 1.9→12 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / σ(F): 3 / Rfactor obs: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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