+Open data
-Basic information
Entry | Database: PDB / ID: 6j4t | ||||||
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Title | Crystal structure of arabidopsis ADAL complexed with IMP | ||||||
Components | Adenosine/AMP deaminase family protein | ||||||
Keywords | HYDROLASE / m6A / N6-mAMP / arabidopsis / Zn / GMP / complex / deaminase | ||||||
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: 1.82 Å | ||||||
Authors | Wu, B.X. / Zhang, D. / Nie, H.B. / Shen, S.L. / Li, S.S. / Patel, D.J. | ||||||
Citation | Journal: Rna Biol. / Year: 2019 Title: Structure ofArabidopsis thaliana N6-methyl-AMP deaminase ADAL with bound GMP and IMP and implications forN6-methyl-AMP recognition and processing. Authors: Wu, B. / Zhang, D. / Nie, H. / Shen, S. / Li, Y. / Li, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j4t.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j4t.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 6j4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/6j4t ftp://data.pdbj.org/pub/pdb/validation_reports/j4/6j4t | HTTPS FTP |
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-Related structure data
Related structure data | 6iv5C 6j23SC 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: 40002.715 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-IMP / |
#3: Chemical | ChemComp-ZN / |
#4: 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: 2.26 Å3/Da / Density % sol: 45.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 32042 / % possible obs: 96.8 % / Redundancy: 10.6 % / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.82→1.92 Å / Rmerge(I) obs: 0.135 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J23 Resolution: 1.82→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.82 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / 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: 21.786 Å2
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Refinement step | Cycle: 1 / Resolution: 1.82→30 Å
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Refine LS restraints |
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