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Yorodumi- PDB-6ijn: The D295N mutant of the N6-methyl-AMP deaminase from Arabidopsis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ijn | |||||||||
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Title | The D295N mutant of the N6-methyl-AMP deaminase from Arabidopsis thaliana complexed with N6m-AMP | |||||||||
Components | Adenosine/AMP deaminase family protein | |||||||||
Keywords | HYDROLASE / Purine metabolism / deaminase / N6-methyladensosine / Tim-barrel / inosine / epigenetics | |||||||||
Function / homology | Function and homology information N6-methyl-AMP deaminase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / deaminase activity / nucleotide metabolic process / RNA catabolic process / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | |||||||||
Authors | Xie, W. / Jia, Q. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Alternative conformation induced by substrate binding for Arabidopsis thalianaN6-methyl-AMP deaminase. Authors: Jia, Q. / Xie, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ijn.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ijn.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ijn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/6ijn ftp://data.pdbj.org/pub/pdb/validation_reports/ij/6ijn | HTTPS FTP |
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-Related structure data
Related structure data | 6ijmC 6ijpC 2adaS 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
#1: Protein | Mass: 42492.453 Da / Num. of mol.: 1 / Mutation: D295N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g04880, T4B21.20, T4B21_20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LPL7 |
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#2: Chemical | ChemComp-6MZ / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32% PEG 3350, 0.1 M NaCl, 0.1 M Tris-HCl (pH 9.0). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. obs: 42279 / % possible obs: 99.7 % / Observed criterion σ(I): 0.051 / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 13 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 4139 / CC1/2: 0.959 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ADA Resolution: 1.66→43.268 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→43.268 Å
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Refine LS restraints |
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LS refinement shell |
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