+Open data
-Basic information
Entry | Database: PDB / ID: 1szi | ||||||
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Title | Crystal Structure of the C-terminus of TIP47 | ||||||
Components | mannose-6-phosphate receptor binding protein 1 | ||||||
Keywords | LIPID BINDING / PEPTIDE BINDING / 4-helix bundle / alpha/beta domain / PAT protein | ||||||
Function / homology | Function and homology information Retrograde transport at the Trans-Golgi-Network / positive regulation of sequestering of triglyceride / lipid storage / lipid droplet / endosome membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.8 Å | ||||||
Authors | Hickenbottom, S.J. / Kimmel, A.R. / Londos, C. / Hurley, J.H. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Structure of a Lipid Droplet Protein: The PAT Family Member TIP47 Authors: Hickenbottom, S.J. / Kimmel, A.R. / Londos, C. / Hurley, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1szi.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1szi.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 1szi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1szi_validation.pdf.gz | 364.1 KB | Display | wwPDB validaton report |
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Full document | 1szi_full_validation.pdf.gz | 371.2 KB | Display | |
Data in XML | 1szi_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1szi_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/1szi ftp://data.pdbj.org/pub/pdb/validation_reports/sz/1szi | 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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Unit cell |
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-Components
#1: Protein | Mass: 27569.863 Da / Num. of mol.: 1 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: HIS parallel 2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3CodonPlus RIL / References: UniProt: Q9DBG5 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.73 % |
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Crystal grow | Temperature: 293.15 K / pH: 8.5 Details: Sodium Citrate, Tris-HCl, sodium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.8→40 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.902 / SU B: 10.356 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20 /
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