+Open data
-Basic information
Entry | Database: PDB / ID: 6ybe | ||||||
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Title | RNASE 3/1 version2 | ||||||
Components | RNASE 3/1 version2 | ||||||
Keywords | HYDROLASE / RNASE 3/1 version2 / PANCREATIC RIBONUCLEASE | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Fernandez-Millan, P. / Prats-Ejarque, G. / Vazquez-Monteagudo, S. / Boix, E. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Exploring the RNase A scaffold to combine catalytic and antimicrobial activities. Structural characterization of RNase 3/1 chimeras. Authors: Fernandez-Millan, P. / Vazquez-Monteagudo, S. / Boix, E. / Prats-Ejarque, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ybe.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ybe.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ybe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/6ybe ftp://data.pdbj.org/pub/pdb/validation_reports/yb/6ybe | HTTPS FTP |
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-Related structure data
Related structure data | 6ssnC 6ybcC 6ymtC 2k11S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16086.296 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: 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: 39.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium acetate pH 5 and 1 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792568 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792568 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→38.45 Å / Num. obs: 43663 / % possible obs: 92.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 10.73 Å2 / CC1/2: 0.996 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.12→1.14 Å / Num. unique obs: 2247 / CC1/2: 0.966 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2K11 Resolution: 1.14→38.45 Å / SU ML: 0.076 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 15.4717 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→38.45 Å
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Refine LS restraints |
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LS refinement shell |
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