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Yorodumi- PDB-1r3m: Crystal structure of the dimeric unswapped form of bovine seminal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r3m | ||||||
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Title | Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease | ||||||
Components | Ribonuclease, seminal | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / SWAPPING / HINGE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Berisio, R. / Sica, F. / De Lorenzo, C. / Di Fiore, A. / Piccoli, R. / Zagari, A. / Mazzarella, L. | ||||||
Citation | Journal: Febs Lett. / Year: 2003 Title: Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease Authors: Berisio, R. / Sica, F. / De Lorenzo, C. / Di Fiore, A. / Piccoli, R. / Zagari, A. / Mazzarella, L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: BOVINE SEMINAL RIBONUCLEASE: STRUCTURE AT 1.9 A RESOLUTION Authors: Mazzarella, L. / CAPASSO, S. / DE MASI, D. / DI LORENZO, G. / MATTIA, C.A. / ZAGARI, A. #2: Journal: Proteins / Year: 2003 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r3m.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r3m.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 1r3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/1r3m ftp://data.pdbj.org/pub/pdb/validation_reports/r3/1r3m | HTTPS FTP |
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-Related structure data
Related structure data | 1bsrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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) Bos taurus (cattle) / Secretion: SEMINAL FLUID / References: UniProt: P00669, EC: 3.1.27.5 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.59 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: evaporation / pH: 8.4 Details: MPD, ammonium sulfate, pH 8.4, EVAPORATION, temperature 294K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 5, 1998 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. all: 13585 / Num. obs: 13585 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 15.1 / Num. unique all: 2000 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 15 Å |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BSR Resolution: 2.2→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.3 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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LS refinement shell | Resolution: 2.2→2.3 Å /
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Refinement | *PLUS Lowest resolution: 15 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |