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Yorodumi- PDB-2w42: THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w42 | ||||||
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Title | THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT DNA DUPLEX. | ||||||
Components |
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Keywords | PROTEIN/DNA COMPLEX / RNAI / RISC / ARGONAUTE / PIWI DOMAIN / PROTEIN-DNA COMPLEX / PROTEIN-DNA COMPLEX complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Parker, J.S. / Roe, S.M. / Barford, D. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Enhancement of the Seed-Target Recognition Step in RNA Silencing by a Piwi-Mid Domain Protein Authors: Parker, J.S. / Parizotto, E.A. / Wang, M. / Roe, S.M. / Barford, D. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w42.cif.gz | 192.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w42.ent.gz | 149.2 KB | Display | PDB format |
PDBx/mmJSON format | 2w42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w42_validation.pdf.gz | 473.3 KB | Display | wwPDB validaton report |
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Full document | 2w42_full_validation.pdf.gz | 494.9 KB | Display | |
Data in XML | 2w42_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 2w42_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/2w42 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/2w42 | HTTPS FTP |
-Related structure data
Related structure data | 1w9hS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49302.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O28951 #2: DNA chain | Mass: 2402.592 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) #3: DNA chain | Mass: 2441.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.6 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 24, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→32.72 Å / Num. obs: 89928 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.09 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.62 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.09 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.6 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W9H Resolution: 1.9→98.06 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.578 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.139 / 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 / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→98.06 Å
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Refine LS restraints |
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