+Open data
-Basic information
Entry | Database: PDB / ID: 5j39 | ||||||
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Title | Crystal Structure of the extended TUDOR domain from TDRD2 | ||||||
Components | Tudor and KH domain-containing protein | ||||||
Keywords | TRANSCRIPTION / tudor domain / structural genomics consortium / SGC | ||||||
Function / homology | Function and homology information piP-body / pi-body / P granule organization / piRNA processing / male meiotic nuclear division / fertilization / P granule / PIWI-interacting RNA (piRNA) biogenesis / spermatogenesis / mitochondrion / RNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Zhang, H. / Tempel, W. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2. Authors: Zhang, H. / Liu, K. / Izumi, N. / Huang, H. / Ding, D. / Ni, Z. / Sidhu, S.S. / Chen, C. / Tomari, Y. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j39.cif.gz | 171.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j39.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 5j39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j39_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
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Full document | 5j39_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 5j39_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5j39_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/5j39 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/5j39 | HTTPS FTP |
-Related structure data
Related structure data | 6b57C 3fdrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/M35J39 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23631.334 Da / Num. of mol.: 2 / Fragment: unp residues 309-498 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TDRKH, TDRD2 / Plasmid: pET28MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE3 / References: UniProt: Q9Y2W6 #2: Chemical | #3: Chemical | ChemComp-UNX / #4: 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: 2.25 Å3/Da / Density % sol: 45.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 15% PEG-8000, 0.2 M magnesium chloride, 0.1 sodium cacodylate. A putative peptide ligand was added to the protein but not found during crystal structure analysis. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97957 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 29, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→53.8 Å / Num. obs: 30647 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.052 / Rrim(I) all: 0.101 / Net I/σ(I): 12 / Num. measured all: 115581 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FDR Resolution: 1.95→34.11 Å / Cor.coef. Fo:Fc: 0.9452 / Cor.coef. Fo:Fc free: 0.9258 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.139 Details: the structure was solved by molecular replacement (PHASER software) and a model build automatically (ARP/WARP) using data from an isomorphous crystal. Further refinement was performed with ...Details: the structure was solved by molecular replacement (PHASER software) and a model build automatically (ARP/WARP) using data from an isomorphous crystal. Further refinement was performed with the programs REFMAC and AUTOBUSTER. TLS groups were defined by the TLSMD server. Model geometry was validated with phenix.molprobity. Not resolved in this version of the model: peaks in the anomalous difference fourier map near residues Y371/F391/D393 are currently modeled as cacodylate ions, but positive difference density coincides with high B-factors for the ion modeled near TDRD2 chain A. Orientation and identity of these ions remain in question.
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Displacement parameters | Biso max: 99.88 Å2 / Biso mean: 41.99 Å2 / Biso min: 15.47 Å2
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Refinement step | Cycle: final / Resolution: 1.95→34.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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