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- PDB-4wfu: Bovine allergen Bos d 2 in the trigonal space group P3221. -

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Basic information

Entry
Database: PDB / ID: 4wfu
TitleBovine allergen Bos d 2 in the trigonal space group P3221.
ComponentsAllergen Bos d 2
KeywordsALLERGEN / Lipocalin
Function / homology
Function and homology information


odorant binding / small molecule binding / extracellular space
Similarity search - Function
Lipocalin, OBP-like / Lipocalin / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNiemi, M.H. / Rouvinen, J.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland137988 Finland
CitationJournal: Sci Rep / Year: 2015
Title: Dimerization of lipocalin allergens.
Authors: Niemi, M.H. / Rytkonen-Nissinen, M. / Miettinen, I. / Janis, J. / Virtanen, T. / Rouvinen, J.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allergen Bos d 2


Theoretical massNumber of molelcules
Total (without water)17,8681
Polymers17,8681
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.500, 75.500, 95.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Allergen Bos d 2 / Dander major allergen BDA20 / Dermal allergen BDA20 / Lipocalin allergen


Mass: 17867.984 Da / Num. of mol.: 1 / Fragment: UNP Residues 17-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Komagataella pastoris (fungus) / References: UniProt: Q28133
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 4.0 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 31990 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 33.26 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 19.56
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.64 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.7_650)refinement
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJ7

1bj7


Resolution: 1.75→38.48 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 1595 5 %Random
Rwork0.2109 30295 --
obs0.2119 31890 99.1 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.509 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 95.58 Å2 / Biso mean: 38.0664 Å2 / Biso min: 24.25 Å2
Baniso -1Baniso -2Baniso -3
1-8.5473 Å20 Å2-0 Å2
2--8.5473 Å20 Å2
3----17.0946 Å2
Refinement stepCycle: final / Resolution: 1.75→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 0 90 1307
Biso mean---45.29 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061277
X-RAY DIFFRACTIONf_angle_d0.9781736
X-RAY DIFFRACTIONf_chiral_restr0.076193
X-RAY DIFFRACTIONf_plane_restr0.004229
X-RAY DIFFRACTIONf_dihedral_angle_d13.473500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7501-1.80650.37371410.39752680282198
1.8065-1.87110.31641430.32782708285199
1.8711-1.9460.33551420.29222724286699
1.946-2.03460.27251430.22782697284098
2.0346-2.14180.25221430.20422732287599
2.1418-2.2760.28531450.2182742288799
2.276-2.45170.25731440.21452746289099
2.4517-2.69840.21811470.232727892936100
2.6984-3.08870.26391450.23942749289499
3.0887-3.89090.21891480.19682805295399
3.8909-38.48920.19481540.18082923307799

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