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Yorodumi- PDB-4ak8: Structure of F241L mutant of langerin carbohydrate recognition domain. -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ak8 | ||||||
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Title | Structure of F241L mutant of langerin carbohydrate recognition domain. | ||||||
Components | C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER K | ||||||
Keywords | SUGAR BINDING PROTEIN / LANGERHANS CELLS / DC-SIGN / HIV / BIRBECK GRANULES | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Chabrol, E. / Thepaut, M. / Dezutter-Dambuyant, C. / Vives, C. / Marcoux, J. / Kahn, R. / Valadeau-Guilemond, J. / Vachette, P. / Durand, D. / Fieschi, F. | ||||||
Citation | Journal: Biophys.J. / Year: 2015 Title: Alteration of the Langerin Oligomerization State Affects Birbeck Granule Formation. Authors: Chabrol, E. / Thepaut, M. / Dezutter-Dambuyant, C. / Vives, C. / Marcoux, J. / Kahn, R. / Valladeau-Guilemond, J. / Vachette, P. / Durand, D. / Fieschi, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ak8.cif.gz | 143.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ak8.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ak8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ak8_validation.pdf.gz | 462.1 KB | Display | wwPDB validaton report |
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Full document | 4ak8_full_validation.pdf.gz | 482.6 KB | Display | |
Data in XML | 4ak8_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 4ak8_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/4ak8 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/4ak8 | HTTPS FTP |
-Related structure data
Related structure data | 3c22S S: Starting model for refinement |
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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
#1: Protein | Mass: 17888.061 Da / Num. of mol.: 4 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 188-328 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJ71 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, PHE 241 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 241 TO LEU ...ENGINEERED | |
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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: 2.02 Å3/Da / Density % sol: 39.2 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: HANGING DROP METHOD 100 MM MES PH 6.0, 200 MM MGCL2 AND 17% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→19.52 Å / Num. obs: 111133 / % possible obs: 99.2 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.88 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.7 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3C22 Resolution: 1.4→19.52 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.866 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
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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: 18.149 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→19.52 Å
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Refine LS restraints |
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