+Open data
-Basic information
Entry | Database: PDB / ID: 4b9x | ||||||
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Title | Structure of extended Tudor domain TD3 from mouse TDRD1 | ||||||
Components | TUDOR DOMAIN-CONTAINING PROTEIN 1 | ||||||
Keywords | REPLICATION | ||||||
Function / homology | Function and homology information siRNA-mediated retrotransposon silencing by heterochromatin formation / pi-body / P granule organization / piRNA processing / chromatoid body / P granule / germ cell development / meiotic cell cycle / spermatogenesis / ribonucleoprotein complex ...siRNA-mediated retrotransposon silencing by heterochromatin formation / pi-body / P granule organization / piRNA processing / chromatoid body / P granule / germ cell development / meiotic cell cycle / spermatogenesis / ribonucleoprotein complex / synapse / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Mathioudakis, N. / Palencia, A. / Kadlec, J. / Round, A. / Tripsianes, K. / Sattler, M. / Pillai, R.S. / Cusack, S. | ||||||
Citation | Journal: RNA / Year: 2012 Title: The Multiple Tudor Domain-Containing Protein Tdrd1 is a Molecular Scaffold for Mouse Piwi Proteins and Pirna Biogenesis Factors. Authors: Mathioudakis, N. / Palencia, A. / Kadlec, J. / Round, A. / Tripsianes, K. / Sattler, M. / Pillai, R.S. / Cusack, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b9x.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b9x.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 4b9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/4b9x ftp://data.pdbj.org/pub/pdb/validation_reports/b9/4b9x | HTTPS FTP |
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-Related structure data
Related structure data | 4b9wSC S: Starting model for refinement C: citing same article (ref.) |
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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: 25383.926 Da / Num. of mol.: 1 / Fragment: EXTENDED TUDOR DOMAIN TD3, RESIDUES 692-917 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q99MV1 |
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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: 2.92 Å3/Da / Density % sol: 57.9 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Details: 10 % PEG 1000 AND 10 % PEG 8000 AT 20C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 6968 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.87 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.06 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.75 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 4B9W Resolution: 2.8→45.63 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.194 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 1.164 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 59.078 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→45.63 Å
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Refine LS restraints |
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