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- PDB-1bj7: BOVINE LIPOCALIN ALLERGEN BOS D 2 -

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Basic information

Entry
Database: PDB / ID: 1bj7
TitleBOVINE LIPOCALIN ALLERGEN BOS D 2
ComponentsD 2
KeywordsALLERGEN / LIPOCALIN
Function / homology
Function and homology information


odorant binding / small molecule binding / extracellular space
Similarity search - Function
Lipocalin, OBP-like / Lipocalin / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRouvinen, J.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Probing the molecular basis of allergy. three-dimensional structure of the bovine lipocalin allergen Bos d 2.
Authors: Rouvinen, J. / Rautiainen, J. / Virtanen, T. / Zeiler, T. / Kauppinen, J. / Taivainen, A. / Mantyjarvi, R.
History
DepositionJul 2, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
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

Downloads & links

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Assembly

Deposited unit
A: D 2


Theoretical massNumber of molelcules
Total (without water)17,8681
Polymers17,8681
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.000, 55.600, 77.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D 2 / DANDER MAJOR ALLERGEN BDA20 / DERMAL ALLERGEN BDA20


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growpH: 4 / Details: pH 4
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Rautiainen, J., (1998) Biochem. Biophys. Res. Commun., 247, 746.
PH range low: 4.5 / PH range high: 3.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein1drop
210 %(w/w)PEG60001reservoir
30.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 8, 1998
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→99 Å / Num. obs: 41606 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.066
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.542 / % possible all: 60.3
Reflection
*PLUS
Num. obs: 14230 / Num. measured all: 41606

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUP

1mup


Resolution: 1.8→8 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1258 10 %RANDOM
Rwork0.184 ---
obs0.184 12707 92.3 %-
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 76 1295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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