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- PDB-5nzb: A disulfide switch determines proteolytic resistance in the birch... -

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Basic information

Entry
Database: PDB / ID: 5nzb
TitleA disulfide switch determines proteolytic resistance in the birch pollen allergen Bet v 2
ComponentsProfilin-2
KeywordsALLERGEN / Profilin / disulfide / Bet v 2
Function / homology
Function and homology information


actin monomer binding / cell cortex / cytoskeleton
Similarity search - Function
Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBetula pendula (European white birch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å
AuthorsSoh, W.T. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fundproject W_01213 Austria
CitationJournal: Int J Mol Sci / Year: 2017
Title: Two Distinct Conformations in Bet v 2 Determine Its Proteolytic Resistance to Cathepsin S.
Authors: Soh, W.T. / Briza, P. / Dall, E. / Asam, C. / Schubert, M. / Huber, S. / Aglas, L. / Bohle, B. / Ferreira, F. / Brandstetter, H.
History
DepositionMay 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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

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Assembly

Deposited unit
A: Profilin-2


Theoretical massNumber of molelcules
Total (without water)14,1601
Polymers14,1601
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.763, 57.336, 59.041
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 Profilin-2 / Allergen Bet v II / Pollen allergen Bet v 2


Mass: 14160.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: A4K9Z8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.9 Å3/Da / Density % sol: 35.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.69→41.13 Å / Num. obs: 12513 / % possible obs: 99.6 % / Redundancy: 16.12 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.082 / Net I/σ(I): 20.21
Reflection shellResolution: 1.69→1.8 Å / Redundancy: 16.47 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 4.37 / Rrim(I) all: 0.66 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CQA

1cqa


Resolution: 1.695→28.668 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2244 640 5.14 %
Rwork0.1948 --
obs0.1962 12447 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.695→28.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 0 99 1093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091046
X-RAY DIFFRACTIONf_angle_d0.9891420
X-RAY DIFFRACTIONf_dihedral_angle_d12.149620
X-RAY DIFFRACTIONf_chiral_restr0.058151
X-RAY DIFFRACTIONf_plane_restr0.005189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6951-1.8260.32231230.25332315X-RAY DIFFRACTION99
1.826-2.00970.27751280.21152307X-RAY DIFFRACTION99
2.0097-2.30040.25231410.20132321X-RAY DIFFRACTION100
2.3004-2.89780.24621380.2142349X-RAY DIFFRACTION99
2.8978-28.67210.17761100.17572515X-RAY DIFFRACTION100

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