+Open data
-Basic information
Entry | Database: PDB / ID: 6tcd | ||||||
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Title | Crystal structure of Salmo salar RidA-2 | ||||||
Components | Ribonuclease UK114 | ||||||
Keywords | UNKNOWN FUNCTION / RidA / Imine Deaminase / YigF/YER057c/UK114 | ||||||
Function / homology | 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate/2-iminopropanoate deaminase / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / ACETATE ION / 2-iminobutanoate/2-iminopropanoate deaminase Function and homology information | ||||||
Biological species | Salmo salar (Atlantic salmon) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Ricagno, S. / Visentin, C. / Di Pisa, F. / Digiovanni, S. / Oberti, L. / Degani, G. / Popolo, L. / Bartorelli, A. | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Two novel fish paralogs provide insights into the Rid family of imine deaminases active in pre-empting enamine/imine metabolic damage. Authors: Digiovanni, S. / Visentin, C. / Degani, G. / Barbiroli, A. / Chiara, M. / Regazzoni, L. / Di Pisa, F. / Borchert, A.J. / Downs, D.M. / Ricagno, S. / Vanoni, M.A. / Popolo, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tcd.cif.gz | 351.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tcd.ent.gz | 255.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tcd_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 6tcd_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 6tcd_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 6tcd_validation.cif.gz | 55 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/6tcd ftp://data.pdbj.org/pub/pdb/validation_reports/tc/6tcd | HTTPS FTP |
-Related structure data
Related structure data | 6tccC 1oniS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14717.908 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmo salar (Atlantic salmon) / Gene: UK114 / Production host: Escherichia coli (E. coli) / References: UniProt: C0H8I4 #2: Chemical | ChemComp-ACT / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.27 Å3/Da / Density % sol: 45.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.5, 25% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→83.1 Å / Num. obs: 114968 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 15.11 Å2 / CC1/2: 1 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.36→1.47 Å / Num. unique obs: 5748 / CC1/2: 0.628 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ONI Resolution: 1.36→43.97 Å / SU ML: 0.1248 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0369
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→43.97 Å
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Refine LS restraints |
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LS refinement shell |
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