+Open data
-Basic information
Entry | Database: PDB / ID: 5yqj | ||||||
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Title | Crystal structure of the first StARkin domain of Lam4 | ||||||
Components | Membrane-anchored lipid-binding protein LAM4 | ||||||
Keywords | TRANSPORT PROTEIN / ligand binding domain / sterol / lipid transport / LTC3 | ||||||
Function / homology | Function and homology information intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / cortical endoplasmic reticulum / cholesterol transfer activity / cholesterol binding / endoplasmic reticulum membrane / mitochondrion / plasma membrane Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Im, Y.J. / Tong, J.S. | ||||||
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 | 5yqj.cif.gz | 231.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yqj.ent.gz | 185 KB | Display | PDB format |
PDBx/mmJSON format | 5yqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yqj_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 5yqj_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 5yqj_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 5yqj_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/5yqj ftp://data.pdbj.org/pub/pdb/validation_reports/yq/5yqj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 20526.432 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: LAM4, LTC3, YHR080C / 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: P38800 #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: 2.06 Å3/Da / Density % sol: 40.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M Na-Citrate-HCl pH 5.0, 30% PEG 1500, 0.1 M Li2SO4 |
-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: Dec 13, 2015 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 80061 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 14.26 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3964 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→29.752 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→29.752 Å
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Refine LS restraints |
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LS refinement shell |
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