+Open data
-Basic information
Entry | Database: PDB / ID: 6tcc | ||||||
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Title | Crystal structure of Salmo salar RidA-1 | ||||||
Components | ribonuclease UK114 | ||||||
Keywords | UNKNOWN FUNCTION / RidA / Imine Deaminase / YigF/YER057c/UK114 | ||||||
Function / homology | Function and homology information 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate/2-iminopropanoate deaminase Similarity search - Function | ||||||
Biological species | Salmo salar (Atlantic salmon) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 | 6tcc.cif.gz | 94.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tcc.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 6tcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tcc_validation.pdf.gz | 870.1 KB | Display | wwPDB validaton report |
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Full document | 6tcc_full_validation.pdf.gz | 870.7 KB | Display | |
Data in XML | 6tcc_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 6tcc_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/6tcc ftp://data.pdbj.org/pub/pdb/validation_reports/tc/6tcc | HTTPS FTP |
-Related structure data
Related structure data | 6tcdC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14241.280 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmo salar (Atlantic salmon) / Gene: hrsp12 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S3KNQ3 |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-PEG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium chloride, 0.2 M Sodium acetate pH 5, 20% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.65 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→42.35 Å / Num. obs: 60156 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 11.74 Å2 / CC1/2: 1 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.05→1.11 Å / Num. unique obs: 8683 / CC1/2: 0.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ONI Resolution: 1.05→33.07 Å / SU ML: 0.0753 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.0811
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→33.07 Å
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Refine LS restraints |
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LS refinement shell |
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