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Yorodumi- PDB-2euk: Crystal Structure of Human Glycolipid Transfer Protein complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2euk | ||||||
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Title | Crystal Structure of Human Glycolipid Transfer Protein complexed with 24:1 Galactosylceramide | ||||||
Components | Glycolipid transfer protein | ||||||
Keywords | LIPID TRANSPORT / Protein-glycolipid complex | ||||||
Function / homology | Function and homology information Glycosphingolipid biosynthesis / glycolipid transfer activity / lipid transfer activity / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / glycolipid binding / glycosphingolipid metabolic process / intermembrane lipid transfer / response to immobilization stress ...Glycosphingolipid biosynthesis / glycolipid transfer activity / lipid transfer activity / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / glycolipid binding / glycosphingolipid metabolic process / intermembrane lipid transfer / response to immobilization stress / lipid binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Malinina, L. / Malakhova, M.L. / Kanack, A.T. / Abagyan, R. / Brown, R.E. / Patel, D.J. | ||||||
Citation | Journal: Plos Biol. / Year: 2006 Title: The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. Authors: Malinina, L. / Malakhova, M.L. / Kanack, A.T. / Lu, M. / Abagyan, R. / Brown, R.E. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2euk.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2euk.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 2euk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/2euk ftp://data.pdbj.org/pub/pdb/validation_reports/eu/2euk | HTTPS FTP |
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-Related structure data
Related structure data | 2eumC 2evdC 2evlC 2evsC 2evtC 1sx6S 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 23877.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET30 XA-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZD2 |
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#2: Sugar | ChemComp-GAL / |
-Non-polymers , 4 types, 184 molecules
#3: Chemical | ChemComp-SPH / |
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#4: Chemical | ChemComp-NER / ( |
#5: Chemical | ChemComp-OCT / |
#6: 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: 2.26 Å3/Da / Density % sol: 45.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.5 Details: 15-20% PEG 3350 or 8000, 50 mM potassium phosphate, pH 4.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 17, 2004 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. all: 18350 / Num. obs: 17855 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.049 / Χ2: 1.051 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.503 / Num. unique all: 1709 / Χ2: 1.096 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1SX6 Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.569 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.154 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.713 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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