+Open data
-Basic information
Entry | Database: PDB / ID: 3euy | ||||||
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Title | Crystal Structure of Ribonuclease A in 50% Dioxane | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / RNAse / organic solvents / multiple solvent crystal structures / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted | ||||||
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 / SYNCHROTRON / Resolution: 1.95 Å | ||||||
Authors | Dechene, M. / Wink, G. / Smith, M. / Swartz, P. / Mattos, C. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Multiple solvent crystal structures of ribonuclease A: An assessment of the method Authors: Dechene, M. / Wink, G. / Smith, M. / Swartz, P. / Mattos, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3euy.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3euy.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 3euy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3euy_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 3euy_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | 3euy_validation.xml.gz | 13 KB | Display | |
Data in CIF | 3euy_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/3euy ftp://data.pdbj.org/pub/pdb/validation_reports/eu/3euy | HTTPS FTP |
-Related structure data
Related structure data | 3euxC 3euzC 3ev0C 3ev1C 3ev2C 3ev3C 3ev4C 3ev5C 3ev6C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: pancreas / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | ChemComp-DIO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 4000, sodium citrate, pH 5.0, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. obs: 15668 / % possible obs: 88.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.068 / Χ2: 2.904 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.95→36.34 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
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Solvent computation | Bsol: 27.518 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.43 Å2 / Biso mean: 35.691 Å2 / Biso min: 14.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→36.34 Å
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Refine LS restraints |
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Xplor file |
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