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- PDB-1r5c: X-ray structure of the complex of Bovine seminal ribonuclease swa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r5c | ||||||
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Title | X-ray structure of the complex of Bovine seminal ribonuclease swapping dimer with d(CpA) | ||||||
![]() | Ribonuclease, seminal | ||||||
![]() | HYDROLASE / ribonucleases / protein dynamics / protein structure-function / ligand binding / population shift / 3D domain swapping | ||||||
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 | ![]() ![]() | ||||||
![]() | Merlino, A. / Vitagliano, L. / Sica, F. / Zagari, A. / Mazzarella, L. | ||||||
![]() | ![]() 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. #1: ![]() 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. #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: ![]() 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. #5: ![]() Title: Crystallization of Multiple Forms of Bovine Seminal Ribonuclease: the liganded and Unliganded State | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.5 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.9 KB | Display | ![]() |
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Full document | ![]() | 453.8 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r5dC ![]() 1bsrS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 13632.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.07 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 5.4 Details: 62-64% saturation ammonium sulfate, 8-10% 2-methyl-2,4-pentandiol, dinucleotide-protein molar ratio of 8:1, pH 5.4, MICRO-BATCH, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Nov 10, 2000 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 13184 / Num. obs: 13184 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.279 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BSR Resolution: 2.1→8 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: 2.1→8 Å
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Refine LS restraints |
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