+Open data
-Basic information
Entry | Database: PDB / ID: 3w1y | ||||||
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Title | Crystal structure of T brucei ATG8.2 in complex with E coli S10 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/RIBOSOMAL PROTEIN / Autophage protein 8 / Autophage protein 12 / ubiquitin fold / TRANSPORT PROTEIN-RIBOSOMAL PROTEIN complex | ||||||
Function / homology | Function and homology information cellular response to nitrogen starvation / transcription antitermination factor activity, RNA binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / autophagy / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding ...cellular response to nitrogen starvation / transcription antitermination factor activity, RNA binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / autophagy / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / structural constituent of ribosome / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Yuan, Y.A. / Wang, C. | ||||||
Citation | Journal: To be Published Title: Crystal structure of T brucei ATG8.2 Authors: Yuan, Y.A. / Wang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w1y.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w1y.ent.gz | 110 KB | Display | PDB format |
PDBx/mmJSON format | 3w1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w1y_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 3w1y_full_validation.pdf.gz | 449.1 KB | Display | |
Data in XML | 3w1y_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 3w1y_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/3w1y ftp://data.pdbj.org/pub/pdb/validation_reports/w1/3w1y | HTTPS FTP |
-Related structure data
Related structure data | 3h9dS 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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-Components
#1: Protein | Mass: 15633.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.7.3320 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57WE7 #2: Protein | | Mass: 11755.597 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpsJ, nusE, b3321, JW3283 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R5 #3: 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: 2.16 Å3/Da / Density % sol: 43.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG3350, MPD, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 15654 / Num. obs: 15654 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.329 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3h9d Resolution: 2.3→44.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.219 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.245 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.511 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→44.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.296→2.356 Å / Total num. of bins used: 20
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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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