+Open data
-Basic information
Entry | Database: PDB / ID: 3h9d | ||||||
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Title | Crystal Structure of Trypanosoma brucei ATG8 | ||||||
Components | Microtubule-associated protein 1A/1B, light chain 3, putative | ||||||
Keywords | STRUCTURAL PROTEIN / autophagy / lipidation / ubiquitin-like / Trypanosoma brucei | ||||||
Function / homology | Function and homology information cellular response to nitrogen starvation / phagophore assembly site / autophagosome assembly / autophagosome / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Koopmann, R. / Muhammad, K. / Perbandt, M. / Betzel, C. / Duszenko, M. | ||||||
Citation | Journal: Autophagy / Year: 2009 Title: Trypanosoma brucei ATG8: structural insights into autophagic-like mechanisms in protozoa. Authors: Koopmann, R. / Muhammad, K. / Perbandt, M. / Betzel, C. / Duszenko, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h9d.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h9d.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 3h9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h9d_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 3h9d_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 3h9d_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 3h9d_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/3h9d ftp://data.pdbj.org/pub/pdb/validation_reports/h9/3h9d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13668.503 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: PPROEX-HTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q582K6 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55.02 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 3 uL of the protein solution (8 mg ml-1 protein in 100 mM Tris/HCl buffer, pH 6.5) with 3 uL of precipitating solution (22% v/v PEG 4000, 200 mM ammonia sulfate, 100 mM MES, pH 6.5). ...Details: 3 uL of the protein solution (8 mg ml-1 protein in 100 mM Tris/HCl buffer, pH 6.5) with 3 uL of precipitating solution (22% v/v PEG 4000, 200 mM ammonia sulfate, 100 mM MES, pH 6.5). Droplets were equilibrated against 500 uL of precipitating solution, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Date: Sep 28, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 13511 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.873 / SU B: 9.099 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.29 / 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 mean: 32.085 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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