+Open data
-Basic information
Entry | Database: PDB / ID: 8qok | ||||||
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Title | Capra hircus reactive intermediate deaminase A mutant - E124A | ||||||
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 / mRNA destabilization / mRNA catabolic process / lipid metabolic process / RNA endonuclease activity, producing 3'-phosphomonoesters / peroxisome / Hydrolases; Acting on ester bonds ...: / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / 2-iminobutanoate/2-iminopropanoate deaminase / mRNA destabilization / mRNA catabolic process / lipid metabolic process / RNA endonuclease activity, producing 3'-phosphomonoesters / peroxisome / 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: 1.2 Å | ||||||
Authors | Rizzi, G. / Visentin, C. / Ricagno, S. | ||||||
Funding support | Italy, 1items
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Citation | Journal: To Be Published Title: Capra hircus reactive intermediate deaminase A mutant - E124A Authors: Rizzi, G. / Visentin, C. / Ricagno, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qok.cif.gz | 198 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qok.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 8qok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qok_validation.pdf.gz | 426.9 KB | Display | wwPDB validaton report |
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Full document | 8qok_full_validation.pdf.gz | 428.3 KB | Display | |
Data in XML | 8qok_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 8qok_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/8qok ftp://data.pdbj.org/pub/pdb/validation_reports/qo/8qok | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14533.599 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: Water | ChemComp-HOH / | |
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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: 1.99 Å3/Da / Density % sol: 38.11 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium sulfate, 0.1 M Bis-Tris propane 7.5, 20 % w/v PEG 3350 |
-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 | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→39.56 Å / Num. obs: 72054 / % possible obs: 100 % / Redundancy: 1.9 % / Biso Wilson estimate: 10.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.037 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.2→1.22 Å / Rmerge(I) obs: 0.388 / Num. unique obs: 3534 / CC1/2: 0.703 / Rrim(I) all: 0.549 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→39.56 Å / SU ML: 0.1058 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7711 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: 18.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→39.56 Å
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Refine LS restraints |
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LS refinement shell |
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