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- PDB-1wrf: Refined solution structure of Der f 2, The Major Mite Allergen fr... -

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Basic information

Entry
Database: PDB / ID: 1wrf
TitleRefined solution structure of Der f 2, The Major Mite Allergen from Dermatophagoides farinae
ComponentsMite group 2 allergen Der f 2
KeywordsALLERGEN / IMMUNOGLOBULIN FOLD
Function / homology
Function and homology information


sterol binding / sterol transport / extracellular region
Similarity search - Function
Sterol transport protein NPC2-like / Immunoglobulin-like - #770 / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mite group 2 allergen Der f 2
Similarity search - Component
Biological speciesDermatophagoides farinae (American house dust mite)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsIchikawa, 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
DepositionOct 15, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mite group 2 allergen Der f 2


Theoretical massNumber of molelcules
Total (without water)14,0641
Polymers14,0641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100LEAST FNOE+FCDIH+FREPEL
RepresentativeModel #1minimized average structure

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Components

#1: Protein Mite group 2 allergen Der f 2 / Der f II


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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 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
Sample conditionspH: 5.6 / Pressure: 1 atm / Temperature: 328 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 1854 NOE-derived distance constraints and 132 dihedral angle restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: LEAST FNOE+FCDIH+FREPEL / Conformers calculated total number: 100 / Conformers submitted total number: 11

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