+Open data
-Basic information
Entry | Database: PDB / ID: 5yqi | ||||||
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Title | Crystal structure of the first StARkin domain of Lam2 | ||||||
Components | Membrane-anchored lipid-binding protein YSP2 | ||||||
Keywords | TRANSPORT PROTEIN / ligand binding domain / sterol / lipid transport | ||||||
Function / homology | Function and homology information intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / cortical endoplasmic reticulum / cell periphery / mitochondrial membrane / apoptotic process / endoplasmic reticulum membrane / mitochondrion ...intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / cortical endoplasmic reticulum / cell periphery / mitochondrial membrane / apoptotic process / endoplasmic reticulum membrane / mitochondrion / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Tong, J. / Im, Y.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites Authors: Tong, J. / Manik, M.K. / Im, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yqi.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yqi.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 5yqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/5yqi ftp://data.pdbj.org/pub/pdb/validation_reports/yq/5yqi | HTTPS FTP |
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-Related structure data
Related structure data | 5yqjSC 5yqpC 5yqqC 5yqrC 5ys0C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19244.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pHis2-Thr Details (production host): an N-terminal hexa-histidine tag fusion Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06681 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES-NaOH pH 6.0, 30% PEG3350, 0.1M KNO3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 22632 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 45.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1117 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YQJ Resolution: 1.6→23.973 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→23.973 Å
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Refine LS restraints |
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LS refinement shell |
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