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- PDB-1xwv: Structure of the house dust mite allergen Der f 2: Implications f... -

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Basic information

Entry
Database: PDB / ID: 1xwv
TitleStructure of the house dust mite allergen Der f 2: Implications for function and molecular basis of IgE cross-reactivity
ComponentsDer f II
KeywordsALLERGEN / BETA SHEETS
Function / homology
Function and homology information


sterol transport / sterol binding / 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
Chem-PE3 / Mite group 2 allergen Der f 2
Similarity search - Component
Biological speciesDermatophagoides farinae (American house dust mite)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsJohannessen, B.R. / Skov, L.K. / Kastrup, J.S. / Kristensen, O. / Bolwig, C. / Larsen, J.N. / Spangfort, M. / Lund, K. / Gajhede, M.
CitationJournal: Febs Lett. / Year: 2005
Title: Structure of the house dust mite allergen Der f 2: implications for function and molecular basis of IgE cross-reactivity.
Authors: Johannessen, B.R. / Skov, L.K. / Kastrup, J.S. / Kristensen, O. / Bolwig, C. / Larsen, J.N. / Spangfort, M. / Lund, K. / Gajhede, M.
History
DepositionNov 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Der f II
B: Der f II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2024
Polymers28,1082
Non-polymers1,0932
Water4,324240
1
A: Der f II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6892
Polymers14,0541
Non-polymers6351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Der f II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5132
Polymers14,0541
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.712, 47.638, 48.275
Angle α, β, γ (deg.)85.98, 75.90, 82.76
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Der f II / mite allergen Der f II


Mass: 14054.177 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides farinae (American house dust mite)
Plasmid: pGAPZalpha-A / Production host: Pichia pastoris (fungus) / References: UniProt: Q00855
#2: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#3: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL / Polyethylene glycol


Mass: 458.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 37.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, potassium citrate, ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 5, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→24.43 Å / Num. all: 18043 / Num. obs: 18043 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 9
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / Num. unique all: 2626 / Rsym value: 0.24 / % possible all: 85.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KTJ

1ktj


Resolution: 1.83→24.43 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 923 -RANDOM
Rwork0.221 ---
obs0.221 18043 93.4 %-
all-18043 --
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.17 Å2-2.15 Å2-1.26 Å2
2--2.2 Å21.11 Å2
3----7.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.83→24.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 74 240 2329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d29.4
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 1.83→1.94 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.322 149 -
Rwork0.309 --
obs--85.9 %

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