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Yorodumi- PDB-2bgg: The structure of a Piwi protein from Archaeoglobus fulgidus compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bgg | ||||||
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Title | The structure of a Piwi protein from Archaeoglobus fulgidus complexed with a 16nt siRNA duplex. | ||||||
Components |
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Keywords | RNA-BINDING PROTEIN/RNA / RNA-BINDING PROTEIN-RNA COMPLEX / RNA-BINDING ARGONAUTE / PIWI DOMAIN / RNAI / RISC / PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Parker, J.S. / Roe, S.M. / Barford, D. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structural Insights Into Mrna Recognition from a Piwi Domain-Sirna Guide Complex Authors: Parker, J.S. / Roe, S.M. / Barford, D. #1: Journal: Embo J. / Year: 2004 Title: Crystal Structure of a Piwi Protein Suggests Mechanisms for Sirna Recognition and Slicer Activity. Authors: Parker, J.S. / 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 | 2bgg.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bgg.ent.gz | 157.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bgg_validation.pdf.gz | 489.8 KB | Display | wwPDB validaton report |
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Full document | 2bgg_full_validation.pdf.gz | 519.9 KB | Display | |
Data in XML | 2bgg_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 2bgg_validation.cif.gz | 58 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/2bgg ftp://data.pdbj.org/pub/pdb/validation_reports/bg/2bgg | 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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Details | THIS STRUCTURE CONTAINS A MONOMERIC PROTEIN, BOUND TO ARNA DUPLEX |
-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: RNA chain | Mass: 2502.537 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: RNA chain | Mass: 2527.545 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE DESIGNED IN SILICO | |
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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: 52.7 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→60 Å / Num. obs: 58841 / % possible obs: 96.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.2 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W9H Resolution: 2.2→99.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 32.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→99.01 Å
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Refine LS restraints |
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