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- PDB-1llt: BIRCH POLLEN ALLERGEN BET V 1 MUTANT E45S -

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Basic information

Entry
Database: PDB / ID: 1llt
TitleBIRCH POLLEN ALLERGEN BET V 1 MUTANT E45S
ComponentsPOLLEN ALLERGEN BET V 1
KeywordsALLERGEN / pathogenesis related proteins
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 / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSpangfort, M.D. / Mirza, O. / Ipsen, H. / Van Neerven, R.J. / Gajhede, M. / Larsen, J.N.
CitationJournal: J.Immunol. / Year: 2003
Title: Dominating IgE-binding epitope of Bet v 1, the major allergen of birch pollen, characterized by X-ray crystallography and site-directed mutagenesis.
Authors: Spangfort, M.D. / Mirza, O. / Ipsen, H. / Van Neerven, R.J. / Gajhede, M. / Larsen, J.N.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLLEN ALLERGEN BET V 1


Theoretical massNumber of molelcules
Total (without water)17,3861
Polymers17,3861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.870, 74.940, 120.000
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 POLLEN ALLERGEN BET V 1


Mass: 17385.541 Da / Num. of mol.: 1 / Mutation: E45S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch) / Production host: Pichia pastoris (fungus) / Strain (production host): DH5-alpha / References: UniProt: P15494

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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: 2.06 Å3/Da / Density % sol: 40.28 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.3 / Method: vapor diffusion, sitting drop / Details: Spangfort, M.D., (1996) Proteins., 26. 358.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
22.0 Mammonium sulfate1drop
3100 mMsodium citrate1droppH6.3
40.01 %sodium azide1drop
52.0 Mammonium sulfate1reservoir
6100 mMsodium citrate1reservoirpH6.3

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 26, 1997
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.06→30 Å / Num. all: 2668 / Num. obs: 2668 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Rsym value: 0.173
Reflection shellResolution: 3.06→3.12 Å / Rsym value: 0.377 / % possible all: 86.1
Reflection
*PLUS
Num. measured all: 11258 / Rmerge(I) obs: 0.173
Reflection shell
*PLUS
% possible obs: 86.1 % / Rmerge(I) obs: 0.377

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→30 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 10464.27 / Data cutoff high rms absF: 10464.27 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 234 9.3 %RANDOM
Rwork0.274 ---
obs-2515 89.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.2875 Å2 / ksol: 0.314056 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 0 0 1227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.54
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 27 6.9 %
Rwork0.301 366 -
obs--86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.54

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