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Yorodumi- PDB-3dlb: Crystal structure of the guide-strand-containing Argonaute protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dlb | ||||||
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Title | Crystal structure of the guide-strand-containing Argonaute protein silencing complex | ||||||
Components |
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Keywords | Nucleic Acid Binding Protein/dna / argonaute / PROTEIN-DNA COMPLEX / Plasmid / Nucleic Acid Binding Protein-dna COMPLEX | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / clearance of foreign intracellular DNA / DNA endonuclease activity / manganese ion binding / DNA replication / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Wang, Y. / Sheng, G. / Patel, D.J. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Structure of the guide-strand-containing argonaute silencing complex. Authors: Wang, Y. / Sheng, G. / Juranek, S. / Tuschl, T. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dlb.cif.gz | 254.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dlb.ent.gz | 201.6 KB | Display | PDB format |
PDBx/mmJSON format | 3dlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/3dlb ftp://data.pdbj.org/pub/pdb/validation_reports/dl/3dlb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 6
NCS ensembles :
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-Components
#1: Protein | Mass: 76728.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Plasmid: PET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (DE3)pLysS / References: UniProt: Q746M7 #2: DNA chain | Mass: 3124.064 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.59 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 308 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5% PEGMME550, 0.1M KCl, 10mM MgCl2, 50 mM Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 308K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918, 0.97929 | |||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 27, 2007 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. obs: 42559 / Redundancy: 4.5 % / Rsym value: 0.06 / Net I/σ(I): 29.4 | |||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.72 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 34.47 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R: 1.17 / ESU R Free: 0.396 / 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: 54.033 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: B / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
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