+Open data
-Basic information
Entry | Database: PDB / ID: 1j1j | ||||||
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Title | Crystal Structure of human Translin | ||||||
Components | Translin | ||||||
Keywords | DNA BINDING PROTEIN / Testis/brain RNA binding protein / ssDNA binding protein / RNA binding protein | ||||||
Function / homology | Function and homology information endoribonuclease complex / Small interfering RNA (siRNA) biogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / male germ cell nucleus / single-stranded DNA binding / endonuclease activity / DNA recombination / sequence-specific DNA binding / Hydrolases; Acting on ester bonds ...endoribonuclease complex / Small interfering RNA (siRNA) biogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / male germ cell nucleus / single-stranded DNA binding / endonuclease activity / DNA recombination / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / mRNA binding / endoplasmic reticulum / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Sugiura, I. / Sasaki, C. / Hasegawa, T. / Kohno, T. / Sugio, S. / Moriyama, H. / Kasai, M. / Matsuzaki, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of human translin at 2.2 A resolution. Authors: Sugiura, I. / Sasaki, C. / Hasegawa, T. / Kohno, T. / Sugio, S. / Moriyama, H. / Kasai, M. / Matsuzaki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j1j.cif.gz | 189.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j1j.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 1j1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/1j1j ftp://data.pdbj.org/pub/pdb/validation_reports/j1/1j1j | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 27625.498 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pQE9 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q15631 #2: 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: 2.8 Å3/Da / Density % sol: 55.76 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Sodium Formate, Sodium Chloride, Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 5, 2000 |
Radiation | Monochromator: Si III CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.836 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 57661 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 8420 / Rsym value: 0.37 / % possible all: 97.3 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 15 Å / Num. obs: 57689 / % possible obs: 97.3 % / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.32 Å / % possible obs: 97.3 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refinement | *PLUS Lowest resolution: 15 Å | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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