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Yorodumi- PDB-1swx: Crystal structure of a human glycolipid transfer protein in apo-form -
+Open data
-Basic information
Entry | Database: PDB / ID: 1swx | ||||||
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Title | Crystal structure of a human glycolipid transfer protein in apo-form | ||||||
Components | Glycolipid transfer protein | ||||||
Keywords | LIPID TRANSPORT / glycosphingolipid intermembrane transfer protein | ||||||
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 / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Malinina, L. / Malakhova, M.L. / Teplov, A. / Brown, R.E. / Patel, D.J. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Structural basis for glycosphingolipid transfer specificity. Authors: Malinina, L. / Malakhova, M.L. / Teplov, A. / 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 | 1swx.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1swx.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 1swx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1swx_validation.pdf.gz | 437.4 KB | Display | wwPDB validaton report |
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Full document | 1swx_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 1swx_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1swx_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/1swx ftp://data.pdbj.org/pub/pdb/validation_reports/sw/1swx | HTTPS FTP |
-Related 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: 23877.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLTP / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZD2 |
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#2: Chemical | ChemComp-HEX / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 3350, potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.65→50 Å / Num. all: 23782 / Num. obs: 23776 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.063 | ||||||||||||||||||
Reflection shell | Resolution: 1.65→1.68 Å / Rmerge(I) obs: 0.34 / Num. unique all: 1051 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.205 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.11 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.075 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20 /
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