+Open data
-Basic information
Entry | Database: PDB / ID: 6etk | ||||||
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Title | Atomic resolution structure of RNase A (data collection 1) | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / Raman microspectroscopy / ribonuclease / atomic resolution / radiation damage / photodamage | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 0.85 Å | ||||||
Authors | Caterino, M. / Vergara, A. / Merlino, A. | ||||||
Citation | Journal: Int. J. Biol. Macromol. / Year: 2018 Title: Raman-markers of X-ray radiation damage of proteins. Authors: Vergara, A. / Caterino, M. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6etk.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6etk.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 6etk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/6etk ftp://data.pdbj.org/pub/pdb/validation_reports/et/6etk | HTTPS FTP |
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-Related structure data
Related structure data | 6etlC 6etmC 6etnC 6etpC 6etqC 6etrC 1kf3S 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: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 | ||
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#2: Chemical | #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: 2.04 Å3/Da / Density % sol: 39.68 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 5.3 Details: Free-interface diffusion of a 10 uL of 30 mg ml-1 protein solution, 20 mM sodium citrate at pH 5.3 agaist 10 ul isopropanol 99.9% isopropanol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 0.85→50 Å / Num. obs: 92774 / % possible obs: 96 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 0.85→0.88 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.2 / % possible all: 86.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KF3 Resolution: 0.85→50 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 15.57 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.85→50 Å
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