+Open data
-Basic information
Entry | Database: PDB / ID: 6ser | ||||||
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Title | Crystal structure of human STARD10 | ||||||
Components | START domain-containing protein 10 | ||||||
Keywords | LIPID TRANSPORT / STARD10 / lipid transporter / Type 2 diabetes | ||||||
Function / homology | Function and homology information phosphatidylcholine biosynthetic process / intercellular canaliculus / motile cilium / lipid transport / Synthesis of PC / microvillus / lipid binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.299 Å | ||||||
Authors | Cheng, K. / Wigley, D.B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: The crystal structure of human STARD10 Authors: Cheng, K. / Wigley, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ser.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ser.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ser.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/6ser ftp://data.pdbj.org/pub/pdb/validation_reports/se/6ser | HTTPS FTP |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33093.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STARD10, SDCCAG28, CGI-52 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y365 | ||||||
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#2: Chemical | ChemComp-PO4 / | ||||||
#3: Chemical | ChemComp-PEG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 50% (v/v) PEG 200, 100 mM Sodium phosphate dibasic/ Potassium phosphate monobasic (pH 6.2), 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→60.043 Å / Num. obs: 19758 / % possible obs: 99.9 % / Redundancy: 13 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.29→2.34 Å / Rmerge(I) obs: 0.44 / Num. unique obs: 925 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.299→60.043 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.98 / 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: 134.87 Å2 / Biso mean: 44.8853 Å2 / Biso min: 19.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.299→60.043 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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