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

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Basic information

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


actin binding / cytoskeleton / cytoplasm
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: 1.999 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Profilin-2
B: Profilin-2


Theoretical massNumber of molelcules
Total (without water)28,3202
Polymers28,3202
Non-polymers00
Water1,63991
1
A: Profilin-2


Theoretical massNumber of molelcules
Total (without water)14,1601
Polymers14,1601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Profilin-2


Theoretical massNumber of molelcules
Total (without water)14,1601
Polymers14,1601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.402, 90.521, 83.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 2
Source method: isolated from a genetically manipulated source
Details: Density was not visible from residue 14 to 21. / 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 / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 2.0 M Ammonium sulfate

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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: 1.999→41.59 Å / Num. obs: 19093 / % possible obs: 98.4 % / Redundancy: 5.67 % / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.081 / Net I/σ(I): 14.35
Reflection shellResolution: 2→2.12 Å / Redundancy: 5.63 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 3.13 / Rrim(I) all: 0.605 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NZB

5nzb


Resolution: 1.999→41.586 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2322 958 5.03 %
Rwork0.2058 --
obs0.2071 19057 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.999→41.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 0 91 1955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061904
X-RAY DIFFRACTIONf_angle_d0.9052572
X-RAY DIFFRACTIONf_dihedral_angle_d15.6051110
X-RAY DIFFRACTIONf_chiral_restr0.057279
X-RAY DIFFRACTIONf_plane_restr0.005333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9992-2.10460.28041370.24752525X-RAY DIFFRACTION98
2.1046-2.23640.2521410.222527X-RAY DIFFRACTION98
2.2364-2.40910.27091280.21752566X-RAY DIFFRACTION99
2.4091-2.65150.25011460.21962556X-RAY DIFFRACTION98
2.6515-3.0350.25671380.2242602X-RAY DIFFRACTION100
3.035-3.82340.2331300.19842654X-RAY DIFFRACTION100
3.8234-41.5950.19561380.18862669X-RAY DIFFRACTION97

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