+Open data
-Basic information
Entry | Database: PDB / ID: 3ax1 | ||||||
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Title | Molecular insights into miRNA processing by Arabidopsis Serrate | ||||||
Components | Serrate RNA effector molecule | ||||||
Keywords | PROTEIN BINDING / miRNA processing / serrate | ||||||
Function / homology | Function and homology information nuclear dicing body / ta-siRNA processing / regulation of meristem development / regulation of adaxial/abaxial pattern formation / shoot system development / nuclear cap binding complex / primary miRNA processing / regulation of alternative mRNA splicing, via spliceosome / RNA splicing / mRNA processing ...nuclear dicing body / ta-siRNA processing / regulation of meristem development / regulation of adaxial/abaxial pattern formation / shoot system development / nuclear cap binding complex / primary miRNA processing / regulation of alternative mRNA splicing, via spliceosome / RNA splicing / mRNA processing / nuclear speck / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleolus / DNA binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.74 Å | ||||||
Authors | Yuan, Y.A. / Machida, S. / Chen, H.Y. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2011 Title: Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE Authors: Machida, S. / Chen, H.Y. / Yuan, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ax1.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ax1.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ax1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/3ax1 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/3ax1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40763.832 Da / Num. of mol.: 1 / Fragment: core domain, UNP residues 194-544 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SE, At2g27100, T20P8.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZVD0 |
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#2: Chemical | ChemComp-ZN / |
#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: 2.84 Å3/Da / Density % sol: 56.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG4K, Potassium formate, Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.2814, 1.2818, 1.1 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2009 | ||||||||||||
Radiation | Monochromator: 360 degree with 1 degree oscillation / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. all: 11900 / Num. obs: 11847 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.073 | ||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 3.5 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.74→46.19 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 37.155 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / 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: 77.032 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→46.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.742→2.814 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.3249 Å / Origin y: 48.2307 Å / Origin z: 48.445 Å
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