+Open data
-Basic information
Entry | Database: PDB / ID: 8qov | ||||||
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Title | Capra hircus reactive intermediate deaminase A mutant - I126Y | ||||||
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: 1.6 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: Capra hircus reactive intermediate deaminase A mutant - I126Y 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 | 8qov.cif.gz | 211.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qov.ent.gz | 170.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qov_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8qov_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8qov_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 8qov_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/8qov ftp://data.pdbj.org/pub/pdb/validation_reports/qo/8qov | 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: 14641.651 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: Chemical | ChemComp-NI / | #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-PEG / | #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: 1.99 Å3/Da / Density % sol: 38.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.02 M MgCl hexahydrate, 0.1 M HEPES, 22% w/v poly(acrylic acid sodium salt)5100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 31, 2021 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→39.69 Å / Num. obs: 31014 / % possible obs: 100 % / Redundancy: 41.3 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.07 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 1523 / CC1/2: 0.789 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→36.26 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.547 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.096 / 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 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.982 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→36.26 Å
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