+Open data
-Basic information
Entry | Database: PDB / ID: 5ltd | ||||||
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Title | Phosphate-bound Pichia angusta Atg18 | ||||||
Components | Autophagy-related protein 18 | ||||||
Keywords | LIPID BINDING PROTEIN / membrane bound protein | ||||||
Function / homology | Function and homology information phagophore assembly site membrane / vacuolar membrane / autophagy / protein transport / endosome membrane Similarity search - Function | ||||||
Biological species | Pichia angusta (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Scacioc, A. / Kuhnel, K. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Phopshate-bound Pichia angusta Atg18 Authors: Scacioc, A. / Kuhnel, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ltd.cif.gz | 138 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ltd.ent.gz | 103.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ltd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/5ltd ftp://data.pdbj.org/pub/pdb/validation_reports/lt/5ltd | HTTPS FTP |
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-Related structure data
Related structure data | 5ltgS 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: 58005.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: two phosphate ions bound as ligands to the protein / Source: (gene. exp.) Pichia angusta (fungus) / Gene: ATG18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5QA94 #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-EDO / | #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 grow | Temperature: 293 K / Method: vapor diffusion Details: 20 % (w/V) PEG 8000, 0.2 M NaCl, 0.1 M sodium phosphate dibasic-citric acid pH 4.2 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45 Å / Num. obs: 27376 / % possible obs: 98.3 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.8 |
Reflection shell | Rmerge(I) obs: 0.645 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LTG Resolution: 2.5→45 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.5→45 Å
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