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- PDB-4qip: Crystal Structure of Major Birch Pollen Allergen Bet v 1 isoform ... -

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Basic information

Entry
Database: PDB / ID: 4qip
TitleCrystal Structure of Major Birch Pollen Allergen Bet v 1 isoform a in complex with Sodium Dodecyl Sulfate
ComponentsMajor pollen allergen Bet v 1-A
KeywordsALLERGEN / PR-10 PROTEIN / Bet v 1-like Superfamily / Defense Response / Response to Biotic Stimulus
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Pathogenesis-related protein Bet v I family / Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major pollen allergen Bet v 1-A
Similarity search - Component
Biological speciesBetula pendula (European white birch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsFreier, R.A. / Kofler, S.G. / Brandstetter, H.
CitationJournal: Biophys.J. / Year: 2014
Title: Ligand binding modulates the structural dynamics and compactness of the major birch pollen allergen
Authors: Grutsch, S. / Fuchs, J.E. / Freier, R. / Kofler, S. / Bibi, M. / Asam, C. / Wallner, M. / Ferreira, F. / Brandstetter, H. / Liedl, K.R. / Tollinger, M.
History
DepositionJun 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major pollen allergen Bet v 1-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0904
Polymers17,4621
Non-polymers6293
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.710, 55.590, 37.910
Angle α, β, γ (deg.)90.000, 93.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Major pollen allergen Bet v 1-A / Allergen Bet v I-A


Mass: 17461.594 Da / Num. of mol.: 1 / Fragment: UNP residues 2-160 / Mutation: D125A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch) / Gene: BETVIA, BETVI / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: P15494
#2: Chemical ChemComp-SDS / DODECYL SULFATE


Mass: 266.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O4S / Comment: detergent*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.97 Å3/Da / Density % sol: 37.71 % / Mosaicity: 0.983 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2M AMMONIUM SULFATE 1.5% 2-METHYL-2,4-PENTANDIOL, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.78→37.83 Å / Num. all: 13028 / Num. obs: 13028 / % possible obs: 98.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.38 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.1 / Net I/σ(I): 8.124
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) allNum. measured allNum. unique all% possible all
1.78-1.873.130.322.175793185397.12
1.87-1.993.350.232.075985178798.07
1.99-2.123.420.153.435710166999.24
2.12-2.293.410.152.625376157598.85
2.29-2.513.560.088.055192145999.96
2.51-2.813.510.078.9446381322100
2.81-3.243.450.0610.814050117399.69
3.24-3.973.370.0610.44330898399.84
3.97-5.623.140.0412.87243277499.87
5.62-37.833.520.0316.63152543398.83

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.78 Å37.83 Å
Translation1.78 Å37.83 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.3.20data scaling
PHASER2.5.2phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A88

4a88


Resolution: 2→37.83 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.836 / WRfactor Rfree: 0.3084 / WRfactor Rwork: 0.2685 / FOM work R set: 0.777 / SU B: 11.504 / SU ML: 0.17 / SU R Cruickshank DPI: 0.307 / SU Rfree: 0.2275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2877 445 4.8 %RANDOM
Rwork0.2447 ---
all0.261 9169 --
obs0.2467 8758 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.27 Å2 / Biso mean: 19.636 Å2 / Biso min: 7.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.95 Å2
2--0.34 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2→37.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 39 48 1304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191298
X-RAY DIFFRACTIONr_angle_refined_deg0.9331.9911759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9225166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62925.71456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33915211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.804153
X-RAY DIFFRACTIONr_chiral_restr0.0510.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021969
X-RAY DIFFRACTIONr_mcbond_it2.0771.706643
X-RAY DIFFRACTIONr_mcangle_it2.7062.539804
X-RAY DIFFRACTIONr_scbond_it2.7451.89655
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 30 -
Rwork0.291 642 -
all-672 -
obs--99.41 %
Refinement TLS params.Method: refined / Origin x: 10.1005 Å / Origin y: 1.0657 Å / Origin z: 10.3951 Å
111213212223313233
T0.0091 Å20.0015 Å20.0012 Å2-0.0031 Å2-0.0052 Å2--0.0193 Å2
L0.2985 °20.1256 °20.0327 °2-0.2034 °2-0.1814 °2--0.2573 °2
S-0.0036 Å °-0.0046 Å °0.0178 Å °-0.001 Å °0.0106 Å °0.0109 Å °-0.0018 Å °-0.0168 Å °-0.007 Å °

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