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Yorodumi- PDB-1wrf: Refined solution structure of Der f 2, The Major Mite Allergen fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wrf | ||||||
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Title | Refined solution structure of Der f 2, The Major Mite Allergen from Dermatophagoides farinae | ||||||
Components | Mite group 2 allergen Der f 2 | ||||||
Keywords | ALLERGEN / IMMUNOGLOBULIN FOLD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Dermatophagoides farinae (American house dust mite) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model type details | minimized average | ||||||
Authors | Ichikawa, S. / Takai, T. / Inoue, T. / Yuuki, T. / Okumura, Y. / Ogura, K. / Inagaki, F. / Hatanaka, H. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2005 Title: NMR Study on the Major Mite Allergen Der f 2: Its Refined Tertiary Structure, Epitopes for Monoclonal Antibodies and Characteristics Shared by ML Protein Group Members Authors: Ichikawa, S. / Takai, T. / Inoue, T. / Yuuki, T. / Okumura, Y. / Ogura, K. / Inagaki, F. / Hatanaka, H. #1: Journal: J.Biol.Chem. / Year: 1998 Title: Solution structure of Der f 2, the major mite allergen for atopic diseases Authors: Ichikawa, S. / Hatanaka, H. / Yuuki, T. / Iwamoto, N. / Kojima, S. / Nishiyama, C. / Ogura, K. / Okumura, Y. / Inagaki, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wrf.cif.gz | 468.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wrf.ent.gz | 410 KB | Display | PDB format |
PDBx/mmJSON format | 1wrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/1wrf ftp://data.pdbj.org/pub/pdb/validation_reports/wr/1wrf | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14064.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dermatophagoides farinae (American house dust mite) Plasmid: PFLT1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q00855 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 2.7mM of Der f 2 U-15N,13C; 20mM KH2PO4/Na2HPO4 buffer; 90% H2O, 10% D2O; 140mM N-octyl-b-D-glucoside; 0.01% (w/v) NaN3 Solvent system: 90% H2O-10% D2O, 140mM N-octyl-b-D-glucoside, 0.01% (w/v) NaN3 |
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Sample conditions | pH: 5.6 / Pressure: 1 atm / Temperature: 328 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz |
-Processing
NMR software | Name: X-PLOR / Version: 3.1 / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures are based on 1854 NOE-derived distance constraints and 132 dihedral angle restraints. |
NMR representative | Selection criteria: minimized average structure |
NMR ensemble | Conformer selection criteria: LEAST FNOE+FCDIH+FREPEL / Conformers calculated total number: 100 / Conformers submitted total number: 11 |