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Yorodumi- PDB-3rh1: X-ray Structure of a cis-proline (P114) to alanine variant of Rib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rh1 | ||||||
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Title | X-ray Structure of a cis-proline (P114) to alanine variant of Ribonuclease A | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / PROTEI / ribonuclease fold / ribonuclease / RNA | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Merlino, A. / Balsamo, A. / Mazzarella, L. / Sica, F. | ||||||
Citation | Journal: Biochimie / Year: 2012 Title: Chain termini cross-talk in the swapping process of bovine pancreatic ribonuclease. Authors: Merlino, A. / Picone, D. / Ercole, C. / Balsamo, A. / Sica, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rh1.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rh1.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 3rh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rh1_validation.pdf.gz | 412.3 KB | Display | wwPDB validaton report |
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Full document | 3rh1_full_validation.pdf.gz | 413.6 KB | Display | |
Data in XML | 3rh1_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 3rh1_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/3rh1 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/3rh1 | HTTPS FTP |
-Related structure data
Related structure data | 3ridC 1fs3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13682.289 Da / Num. of mol.: 1 / Mutation: P114A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 35% ammonium sulphate, 50% NaCl, 0.1M sodium acetate pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: ENRAF-NONIUS / Detector: IMAGE PLATE / Date: Dec 12, 2003 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / 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: 8996 / Num. obs: 8996 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.098 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 1FS3 Resolution: 2.1→20 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→20 Å
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