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Open data
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Basic information
Entry | Database: PDB / ID: 5yqr | ||||||
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Title | Crystal structure of the PH-like domain of Lam6 | ||||||
![]() | Endolysin/Membrane-anchored lipid-binding protein LAM6 fusion protein | ||||||
![]() | TRANSPORT PROTEIN / ligand binding domain / sterol / lipid transport / LTC1 | ||||||
Function / homology | ![]() intracellular sterol transport / nucleus-vacuole junction / sterol transfer activity / vacuole-mitochondrion membrane contact site / mitochondria-associated endoplasmic reticulum membrane contact site / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...intracellular sterol transport / nucleus-vacuole junction / sterol transfer activity / vacuole-mitochondrion membrane contact site / mitochondria-associated endoplasmic reticulum membrane contact site / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / membrane => GO:0016020 / defense response to bacterium / endoplasmic reticulum membrane / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tong, J. / Im, Y.J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.8 KB | Display | ![]() |
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PDB format | ![]() | 98.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 681 KB | Display | ![]() |
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Full document | ![]() | 686.1 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yqiC ![]() 5yqjC ![]() 5yqpC ![]() 5yqqC ![]() 5ys0C ![]() 4n9nS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31725.223 Da / Num. of mol.: 1 / Mutation: R12G,D20N, C54T, C97A, I137R Source method: isolated from a genetically manipulated source Details: The N-termial T4 lysozyme (residue 2-160) tag fusion.The intact protein expressed is Hexa-histidine -Thrombin cleavage site - T4 Lysozyme - Lam6 (161-272),The N-termial T4 lysozyme (residue ...Details: The N-termial T4 lysozyme (residue 2-160) tag fusion.The intact protein expressed is Hexa-histidine -Thrombin cleavage site - T4 Lysozyme - Lam6 (161-272),The N-termial T4 lysozyme (residue 2-160) tag fusion. The intact protein expressed is Hexa-histidine -Thrombin cleavage site - T4 Lysozyme - Lam6 (161-272) Source: (gene. exp.) ![]() ![]() ![]() Plasmid: pHis-T4L / Strain: ATCC 204508 / S288c / Gene: LAM6, LTC1, YLR072W Details (production host): N-terminal T4 Lysozyme tag fusion Production host: ![]() ![]() |
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#2: Chemical | ChemComp-2PE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES-HCl pH 7.0, 10% PEG8000, 0.1M Na3Citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 14, 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: 2.4→50 Å / Num. obs: 15204 / % possible obs: 99 % / Redundancy: 8.1 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 48.3 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 9.7 / Num. unique obs: 727 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4N9N Resolution: 2.402→30.374 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.49 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.402→30.374 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 25.0507 Å / Origin y: 56.3488 Å / Origin z: 44.0798 Å
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Refinement TLS group | Selection details: all |