+Open data
-Basic information
Entry | Database: PDB / ID: 2xdy | ||||||
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Title | Crystal structure of the N. crassa QDE-2 AGO MID domain | ||||||
Components | POST-TRANSCRIPTIONAL GENE SILENCING PROTEIN QDE-2RNA interference | ||||||
Keywords | RNA BINDING PROTEIN / ARGONAUTE / GENE SILENCING / RNA-INDUCED SILENCING COMPLEX / 5' END BINDING / ROSSMANN-LIKE FOLD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | NEUROSPORA CRASSA (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Boland, A. / Tritschler, F. / Weichenrieder, O. | ||||||
Citation | Journal: Embo Rep. / Year: 2010 Title: Crystal Structure and Ligand Binding of the Mid Domain of a Eukaryotic Argonaute Protein. Authors: Boland, A. / Tritschler, F. / Heimstaedt, S. / Izaurralde, E. / Weichenrieder, O. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: PROVIDED BY DEPOSITOR. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xdy.cif.gz | 38.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xdy.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/2xdy ftp://data.pdbj.org/pub/pdb/validation_reports/xd/2xdy | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15978.780 Da / Num. of mol.: 1 / Fragment: MID DOMAIN, RESIDUES 506-646 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PETM60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9P8T1 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence details | THE FIRST 4 AMINO ACIDS (GAMA) ARISE FROM THE CLONING SITE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 7.2 / Details: 200 MM AMMONIUM SULFATE 16% PEG4000, pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→60.2 Å / Num. obs: 8285 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 41.9 Å2 / Rsym value: 0.05 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.94 / Rsym value: 0.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.2→31.288 Å / SU ML: 0.29 / Phase error: 20.89 / Stereochemistry target values: ML Details: THE RESIDUES ARISEING FROM THE CLONING SITE AS WELL AS RESIDUES 506 - 513 AND RESIDUES 641 - 646 ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.801 Å2 / ksol: 0.369 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→31.288 Å
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Refine LS restraints |
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LS refinement shell |
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