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Yorodumi- PDB-3c22: Crystal structure of the carbohydrate recognition domain of human... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c22 | ||||||
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Title | Crystal structure of the carbohydrate recognition domain of human Langerin | ||||||
Components | C-type lectin domain family 4 member K | ||||||
Keywords | IMMUNE SYSTEM / SUGAR BINDING PROTEIN / C-type lectin domain / Coiled coil / Glycoprotein / Membrane / Signal-anchor / Transmembrane | ||||||
Function / homology | Function and homology information Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / endocytic vesicle / clathrin-coated endocytic vesicle membrane / signaling receptor activity / early endosome membrane / carbohydrate binding / defense response to virus / external side of plasma membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å | ||||||
Authors | Thepaut, M. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural studies of langerin and Birbeck granule: a macromolecular organization model Authors: Thepaut, M. / Valladeau, J. / Nurisso, A. / Kahn, R. / Arnou, B. / Vives, C. / Saeland, S. / Ebel, C. / Monnier, C. / Dezutter-Dambuyant, C. / Imberty, A. / Fieschi, F. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Overproduction, purification and preliminary crystallographic analysis of the carbohydrate-recognition domain of human langerin Authors: Thepaut, M. / Vives, C. / Pompidor, G. / Kahn, R. / Fieschi, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c22.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c22.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 3c22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c22_validation.pdf.gz | 460.5 KB | Display | wwPDB validaton report |
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Full document | 3c22_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 3c22_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 3c22_validation.cif.gz | 48.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/3c22 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/3c22 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 17949.035 Da / Num. of mol.: 4 Fragment: carbohydrate recognition domain, UNP residues 188-328 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD207 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UJ71 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MG / #4: 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: 1.99 Å3/Da / Density % sol: 38.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 400mM MgCl2, 25% PEG 3350, 100mM HEPES pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97966 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97966 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 90252 / Num. obs: 89721 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 6.1 / Num. unique all: 14378 / Rsym value: 0.331 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.5→47.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 Isotropic thermal model: Isotropic except for Ca and Mg atoms Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.091 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.873 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→47.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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