[English] 日本語
Yorodumi- PDB-11bg: A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING IN BO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 11bg | ||||||
---|---|---|---|---|---|---|---|
Title | A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING IN BOVINE SEMINAL RIBONUCLEASE | ||||||
Components | PROTEIN (BOVINE SEMINAL RIBONUCLEASE) | ||||||
Keywords | HYDROLASE / PHOSPHORIC DIESTER / RNA | ||||||
Function / homology | Function and homology information : / 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 | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.9 Å | ||||||
Authors | Vitagliano, L. / Adinolfi, S. / Sica, F. / Merlino, A. / Zagari, A. / Mazzarella, L. | ||||||
Citation | 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. #1: Journal: J.Cryst.Growth / Year: 1999 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: 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. #3: Journal: J.Cryst.Growth / Year: 1997 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: 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 11bg.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb11bg.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 11bg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/1b/11bg ftp://data.pdbj.org/pub/pdb/validation_reports/1b/11bg | HTTPS FTP |
---|
-Related structure data
Related structure data | 1bsrS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-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) Bos taurus (cattle) References: UniProt: RNS_BOVIN, UniProt: P00669*PLUS, EC: 3.1.27.5 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-U2G / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.68 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / σ(F): 3 / Rfactor obs: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|