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Yorodumi- PDB-2evd: Crystal structure of human Glycolipid Transfer Protein complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2evd | |||||||||
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Title | Crystal structure of human Glycolipid Transfer Protein complexed with 12:0 Lactosylceramide | |||||||||
Components | Glycolipid transfer protein | |||||||||
Keywords | LIPID TRANSPORT / protein-glycolipid complex | |||||||||
Function / homology | Function and homology information glycolipid transfer activity / lipid transfer activity / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / Glycosphingolipid transport / glycolipid binding / intermembrane lipid transfer / response to immobilization stress / lipid binding ...glycolipid transfer activity / lipid transfer activity / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / Glycosphingolipid transport / glycolipid binding / 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: 2 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 | 2evd.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2evd.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 2evd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2evd_validation.pdf.gz | 932.5 KB | Display | wwPDB validaton report |
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Full document | 2evd_full_validation.pdf.gz | 933.6 KB | Display | |
Data in XML | 2evd_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 2evd_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/2evd ftp://data.pdbj.org/pub/pdb/validation_reports/ev/2evd | HTTPS FTP |
-Related structure data
Related structure data | 2eukC 2eumSC 2evlC 2evsC 2evtC 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: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
-Non-polymers , 5 types, 174 molecules
#3: Chemical | ChemComp-SPH / |
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#4: Chemical | ChemComp-DAO / |
#5: Chemical | ChemComp-OCT / |
#6: Chemical | ChemComp-D10 / |
#7: 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: 45.65 % |
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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: Dec 9, 2004 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 14549 / Num. obs: 14549 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.058 / Χ2: 1.063 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.602 / Num. unique all: 1446 / Χ2: 1.006 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EUM Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.661 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.176 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.205 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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