+Open data
-Basic information
Entry | Database: PDB / ID: 5brl | ||||||
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Title | Crystal Structure of L124D STARD4 | ||||||
Components | StAR-related lipid transfer protein 4 | ||||||
Keywords | LIPID BINDING PROTEIN / alpha helix grip | ||||||
Function / homology | Function and homology information cholesterol transport involved in cholesterol storage / Pregnenolone biosynthesis / positive regulation of bile acid biosynthetic process / intracellular cholesterol transport / cholesterol import / positive regulation of cholesterol metabolic process / cholesterol transfer activity / cholesterol binding / cytoplasmic vesicle / endoplasmic reticulum ...cholesterol transport involved in cholesterol storage / Pregnenolone biosynthesis / positive regulation of bile acid biosynthetic process / intracellular cholesterol transport / cholesterol import / positive regulation of cholesterol metabolic process / cholesterol transfer activity / cholesterol binding / cytoplasmic vesicle / endoplasmic reticulum / mitochondrion / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å | ||||||
Authors | Iaea, D.B. / Dikiy, I. / Kiburu, I. / Eliezer, D.E. / Maxfield, F.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2015 Title: STARD4 Membrane Interactions and Sterol Binding. Authors: Iaea, D.B. / Dikiy, I. / Kiburu, I. / Eliezer, D. / Maxfield, F.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5brl.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5brl.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 5brl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/5brl ftp://data.pdbj.org/pub/pdb/validation_reports/br/5brl | HTTPS FTP |
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-Related structure data
Related structure data | 1jssS 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: 24110.322 Da / Num. of mol.: 2 / Fragment: UNP residues 13-222 / Mutation: L124D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stard4 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99JV5 #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: 2.49 Å3/Da / Density % sol: 50.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1 M MES pH 6.2, 2.2 M ammonium sulfate |
-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: Sep 11, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→50 Å / Num. obs: 26090 / % possible obs: 80.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.512 / Net I/av σ(I): 16.154 / Net I/σ(I): 13.6 / Num. measured all: 65905 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JSS Resolution: 2.003→39.426 Å / FOM work R set: 0.8377 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.27 Å2 / Biso mean: 21.54 Å2 / Biso min: 9.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.003→39.426 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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