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Yorodumi- PDB-3hup: High-resolution structure of the extracellular domain of human CD69 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hup | ||||||
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Title | High-resolution structure of the extracellular domain of human CD69 | ||||||
Components | Early activation antigen CD69 | ||||||
Keywords | IMMUNE SYSTEM / C-TYPE LECTIN-LIKE DOMAIN / Disulfide bond / Glycoprotein / Lectin / Membrane / Phosphoprotein / Signal-anchor / Transmembrane | ||||||
Function / homology | Function and homology information transmembrane signaling receptor activity / cellular response to xenobiotic stimulus / carbohydrate binding / external side of plasma membrane / protein-containing complex / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS / Resolution: 1.371 Å | ||||||
Authors | Kolenko, P. / Dohnalek, J. / Skalova, T. / Hasek, J. / Duskova, J. / Vanek, O. / Bezouska, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: The high-resolution structure of the extracellular domain of human CD69 using a novel polymer Authors: Kolenko, P. / Skalova, T. / Vanek, O. / Stepankova, A. / Duskova, J. / Hasek, J. / Bezouska, K. / Dohnalek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hup.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hup.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 3hup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hup_validation.pdf.gz | 429.2 KB | Display | wwPDB validaton report |
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Full document | 3hup_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 3hup_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 3hup_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/3hup ftp://data.pdbj.org/pub/pdb/validation_reports/hu/3hup | HTTPS FTP |
-Related structure data
Related structure data | 3cckS 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: 15145.969 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, UNP residues 70-199 Source method: isolated from a genetically manipulated source Details: REFOLDING / Source: (gene. exp.) Homo sapiens (human) / Gene: CD69 / Plasmid: pRSETB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3) RIL / References: UniProt: Q07108 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #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: 2.19 Å3/Da / Density % sol: 43.77 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 30% di[polyethyleneglycol]adipate (MW 900), 0.1M Imidazole pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 301K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2007 / Details: 2 mirrors and a double-crystal monochromator |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection twin | Operator: -h-k,k,-l / Fraction: 0.113 |
Reflection | Resolution: 1.37→30 Å / Num. all: 51840 / Num. obs: 51840 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 34.1 |
Reflection shell | Resolution: 1.37→1.4 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2576 / % possible all: 65.8 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS Starting model: PDB ENTRY 3CCK Resolution: 1.371→28.172 Å / FOM work R set: 0.873 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 20.51 / Stereochemistry target values: CCP4 MONOMER LIBRARY / Details: twin refinement
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.242 Å2 / ksol: 0.332 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.94 Å2 / Biso mean: 24.7 Å2 / Biso min: 8.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.371→28.172 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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