+Open data
-Basic information
Entry | Database: PDB / ID: 3fdr | ||||||
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Title | Crystal structure of TDRD2 | ||||||
Components | Tudor and KH domain-containing protein | ||||||
Keywords | RNA BINDING PROTEIN / Tdrd2 / Tudor / Structural Genomics / Structural Genomics Consortium / SGC / Alternative splicing / RNA-binding | ||||||
Function / homology | Function and homology information piP-body / pi-body / P granule organization / piRNA processing / male meiotic nuclear division / P granule / fertilization / PIWI-interacting RNA (piRNA) biogenesis / spermatogenesis / mitochondrion / RNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Amaya, M.F. / Adams, M.A. / Guo, Y. / Li, Y. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. ...Amaya, M.F. / Adams, M.A. / Guo, Y. / Li, Y. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi Authors: Chen, C. / Jin, J. / James, D.A. / Adams-Cioaba, M.A. / Park, J.G. / Guo, Y. / Tenaglia, E. / Xu, C. / Gish, G. / Min, J. / Pawson, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fdr.cif.gz | 32.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fdr.ent.gz | 20.8 KB | Display | PDB format |
PDBx/mmJSON format | 3fdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/3fdr ftp://data.pdbj.org/pub/pdb/validation_reports/fd/3fdr | HTTPS FTP |
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-Related structure data
Related structure data | 2diqS 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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Unit cell |
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-Components
#1: Protein | Mass: 10449.630 Da / Num. of mol.: 1 / Fragment: Tudor domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TDRKH, TDRD2 / Plasmid: pet15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y2W6 |
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#2: 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: 2.09 Å3/Da / Density % sol: 41.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 3350, 0.2M NaCl, 100 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Date: Nov 18, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→40 Å / Num. obs: 8475 / % possible obs: 91 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.072 / Χ2: 1.523 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2DIQ Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.585 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.146 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.64 Å2 / Biso mean: 22.187 Å2 / Biso min: 11.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.793 Å / Total num. of bins used: 20
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