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- PDB-2f08: Crystal structure of a major house dust mite allergen, Derf 2 -

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Basic information

Entry
Database: PDB / ID: 2f08
TitleCrystal structure of a major house dust mite allergen, Derf 2
Componentsmite allergen Der f II
KeywordsIMMUNE SYSTEM / 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
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / Mite group 2 allergen Der f 2
Similarity search - Component
Biological speciesDermatophagoides farinae (American house dust mite)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsMikami, B. / Tanaka, Y. / Minato, N. / Suzuki, M. / Korematsu, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Crystal structure and some properties of a major house dust mite allergen, Derf 2
Authors: Suzuki, M. / Tanaka, Y. / Korematsu, S. / Mikami, B. / Minato, N.
History
DepositionNov 12, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: mite allergen Der f II
B: mite allergen Der f II
C: mite allergen Der f II
D: mite allergen Der f II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5815
Polymers56,2574
Non-polymers3241
Water2,810156
1
A: mite allergen Der f II


Theoretical massNumber of molelcules
Total (without water)14,0641
Polymers14,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mite allergen Der f II


Theoretical massNumber of molelcules
Total (without water)14,0641
Polymers14,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mite allergen Der f II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3892
Polymers14,0641
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mite allergen Der f II


Theoretical massNumber of molelcules
Total (without water)14,0641
Polymers14,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.124, 54.328, 102.354
Angle α, β, γ (deg.)90.00, 91.35, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein
mite allergen Der f II


Mass: 14064.193 Da / Num. of mol.: 4 / Fragment: residues 1-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides farinae (American house dust mite)
Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta(DE3)pLys / References: UniProt: Q00855
#2: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 23% PEG 4000, 0.06M ammonium sulfate, 0.1M sodium acetate, 10mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Dec 21, 1999 / Details: carbon monochrometer
RadiationMonochromator: carbon monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→28.3 Å / Num. all: 34340 / Num. obs: 32658 / % possible obs: 95.05 % / Observed criterion σ(I): 1 / Redundancy: 3.38 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.058 / Net I/σ(I): 25.83
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 3.37 % / Mean I/σ(I) obs: 2.61 / Num. unique all: 3009 / Rsym value: 0.342 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
SAINTdata reduction
SAINTdata scaling
PHASESphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→14.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 942193.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2652 10 %RANDOM
Rwork0.206 ---
obs0.206 26532 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.6915 Å2 / ksol: 0.259142 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å2-0.01 Å2
2--6.73 Å20 Å2
3----4.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 22 156 4120
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d28.3
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it4.511.5
X-RAY DIFFRACTIONc_mcangle_it5.652
X-RAY DIFFRACTIONc_scbond_it7.152
X-RAY DIFFRACTIONc_scangle_it9.552.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 239 10.5 %
Rwork0.297 3372 -
obs-2225 75.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4p4c_xplor.param

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