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- PDB-1r5d: X-ray structure of bovine seminal ribonuclease swapping dimer fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r5d | ||||||
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Title | X-ray structure of bovine seminal ribonuclease swapping dimer from a new crystal form | ||||||
![]() | 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 / 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 | ![]() | 58.6 KB | Display | ![]() |
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PDB format | ![]() | 43.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 371.8 KB | Display | ![]() |
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Full document | ![]() | 374.1 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 9.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r5cC ![]() 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: 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: 46.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, 0.1 M sodium acetate, 0.1 M TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, 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 20, 2000 / Details: mirrors |
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: 2.4→37 Å / Num. all: 10097 / Num. obs: 10097 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.102 |
Reflection shell | Resolution: 2.4→2.52 Å / Rmerge(I) obs: 0.25 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BSR Resolution: 2.5→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: 2.5→8 Å
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Refine LS restraints |
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