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Yorodumi- PDB-3l4r: Crystal structure of the dog lipocalin allergen Can f 2 and impli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l4r | ||||||
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Title | Crystal structure of the dog lipocalin allergen Can f 2 and implications for cross-reactivity to the cat allergen Fel d 4 | ||||||
Components | Minor allergen Can f 2 | ||||||
Keywords | ALLERGEN / LIPID BINDING PROTEIN / lipocalin allergen / Disulfide bond / Secreted / Transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Canis familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Madhurantakam, C. / Nilsson, O.B. / Gronlund, H. / Achour, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal Structure of the Dog Lipocalin Allergen Can f 2: Implications for Cross-reactivity to the Cat Allergen Fel d 4 Authors: Madhurantakam, C. / Nilsson, O.B. / Uchtenhagen, H. / Konradsen, J. / Saarne, T. / Hogbom, E. / Sandalova, T. / Gronlund, H. / Achour, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l4r.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l4r.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 3l4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l4r_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
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Full document | 3l4r_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | 3l4r_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 3l4r_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/3l4r ftp://data.pdbj.org/pub/pdb/validation_reports/l4/3l4r | HTTPS FTP |
-Related structure data
Related structure data | 2r73S 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: 19473.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis familiaris (dog) / Gene: can f 2 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O18874 |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 2.15 Å3/Da / Density % sol: 42.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 60% (w/v) Tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2008 / Details: mirrors |
Radiation | Monochromator: Diamond, Ge / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→34.5 Å / Num. obs: 30546 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.9 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R73 Resolution: 1.45→30.19 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.766 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.054 / 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 max: 47.27 Å2 / Biso mean: 11.678 Å2 / Biso min: 6.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→30.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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