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- PDB-4wfv: Bovine allergen Bos d 2 in the monoclinic space group C2. -

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Basic information

Entry
Database: PDB / ID: 4wfv
TitleBovine allergen Bos d 2 in the monoclinic space group C2.
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: 1.4 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.940, 36.590, 36.470
Angle α, β, γ (deg.)90.000, 95.860, 90.000
Int Tables number5
Space group name H-MC121

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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.: 67 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 2.5 M 1,6-hexanediol, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.011 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 31792 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 12.02 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.037 / Net I/σ(I): 22.3
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.2 / % possible all: 88.8

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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: 1.4→25.603 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 1589 5 %Random
Rwork0.1963 30200 --
obs0.1971 31789 96.93 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.937 Å2 / ksol: 0.476 e/Å3
Displacement parametersBiso max: 55.47 Å2 / Biso mean: 14.0511 Å2 / Biso min: 4.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.2393 Å2-0 Å21.2922 Å2
2--0.6536 Å2-0 Å2
3---0.5858 Å2
Refinement stepCycle: final / Resolution: 1.4→25.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 0 67 1296
Biso mean---20.43 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061276
X-RAY DIFFRACTIONf_angle_d1.0811732
X-RAY DIFFRACTIONf_chiral_restr0.074192
X-RAY DIFFRACTIONf_plane_restr0.005228
X-RAY DIFFRACTIONf_dihedral_angle_d11.712495
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 (%)
1.4-1.44520.35261200.28542273239382
1.4452-1.49680.28511400.25332667280795
1.4968-1.55680.20841470.21482789293699
1.5568-1.62760.23341470.191528022949100
1.6276-1.71340.21831480.18992802295099
1.7134-1.82070.19921490.17622832298199
1.8207-1.96120.20711450.18172767291299
1.9612-2.15850.18281480.17552810295898
2.1585-2.47060.19021470.17452793294098
2.4706-3.11190.22861480.19592813296199
3.1119-25.60760.20951500.20872852300297

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