+Open data
-Basic information
Entry | Database: PDB / ID: 8qou | ||||||
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Title | Reactive intermediate deaminase A mutant - R107K | ||||||
Components | 2-iminobutanoate/2-iminopropanoate deaminase | ||||||
Keywords | UNKNOWN FUNCTION / Enzyme / deaminase | ||||||
Function / homology | Function and homology information 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / 2-iminobutanoate/2-iminopropanoate deaminase / organonitrogen compound catabolic process / mRNA destabilization / mRNA catabolic process / lipid metabolic process / peroxisome / RNA endonuclease activity, producing 3'-phosphomonoesters / Hydrolases; Acting on ester bonds ...2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / 2-iminobutanoate/2-iminopropanoate deaminase / organonitrogen compound catabolic process / mRNA destabilization / mRNA catabolic process / lipid metabolic process / peroxisome / RNA endonuclease activity, producing 3'-phosphomonoesters / Hydrolases; Acting on ester bonds / negative regulation of translation / mitochondrial matrix / mRNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Capra hircus (goat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Rizzi, G. / Visentin, C. / Di Pisa, F. / Ricagno, S. | ||||||
Funding support | Italy, 1items
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Citation | Journal: To Be Published Title: Reactive intermediate deaminase A mutant - R107K Authors: Rizzi, G. / Visentin, C. / Di Pisa, F. / Ricagno, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qou.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qou.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 8qou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qou_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8qou_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8qou_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 8qou_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/8qou ftp://data.pdbj.org/pub/pdb/validation_reports/qo/8qou | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 14563.620 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Capra hircus (goat) / Gene: RIDA / Production host: Escherichia coli (E. coli) References: UniProt: P80601, 2-iminobutanoate/2-iminopropanoate deaminase, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-PEG / | #3: Chemical | ChemComp-EDO / | #4: Chemical | #5: 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: 2.13 Å3/Da / Density % sol: 42.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate trihydrate, pH 6.5, 30% w/v polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45.24 Å / Num. obs: 48575 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC1/2: 0.939 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2408 / CC1/2: 0.588 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→40.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.512 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.93 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→40.5 Å
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