+Open data
-Basic information
Entry | Database: PDB / ID: 7zs6 | ||||||
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Title | Crystal structure of Apis mellifera RidA | ||||||
Components | Reactive intermediate deaminase A | ||||||
Keywords | UNKNOWN FUNCTION / Deiminase / Ractive intermediate deaminase | ||||||
Function / homology | RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / Uncharacterized protein Function and homology information | ||||||
Biological species | Apis mellifera (honey bee) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | ||||||
Authors | Visentin, C. / Rizzi, G. / Ricagno, S. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Apis mellifera RidA, a novel member of the canonical YigF/YER057c/UK114 imine deiminase superfamily of enzymes pre-empting metabolic damage. Authors: Visentin, C. / Rizzi, G. / Degani, G. / Digiovanni, S. / Robecchi, G. / Barbiroli, A. / Popolo, L. / Vanoni, M.A. / Ricagno, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zs6.cif.gz | 195 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zs6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7zs6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zs6_validation.pdf.gz | 413.7 KB | Display | wwPDB validaton report |
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Full document | 7zs6_full_validation.pdf.gz | 417.2 KB | Display | |
Data in XML | 7zs6_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 7zs6_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/7zs6 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/7zs6 | HTTPS FTP |
-Related structure data
Related structure data | 1oniS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 15409.731 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Apis mellifera (honey bee) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7M7GBQ0 #2: Chemical | ChemComp-EDO / | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.29 Å3/Da / Density % sol: 46.22 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M MES, 20% PEG 6000 pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→43.305 Å / Num. obs: 101696 / % possible obs: 99.44 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.31→1.33 Å / Rmerge(I) obs: 1.236 / Num. unique obs: 4890 / CC1/2: 0.404 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ONI Resolution: 1.31→43.305 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.98 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.045 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.816 Å2
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Refinement step | Cycle: LAST / Resolution: 1.31→43.305 Å
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Refine LS restraints |
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LS refinement shell |
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