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- PDB-1fm4: CRYSTAL STRUCTURE OF THE BIRCH POLLEN ALLERGEN BET V 1L -

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Basic information

Entry
Database: PDB / ID: 1fm4
TitleCRYSTAL STRUCTURE OF THE BIRCH POLLEN ALLERGEN BET V 1L
ComponentsMAJOR POLLEN ALLERGEN BET V 1-L
KeywordsALLERGEN / alpha-beta: 6 anti-parallel beta strands and 3 alpha helices.
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-L
Similarity search - Component
Biological speciesBetula pendula (European white birch)
MethodX-RAY DIFFRACTION / Resolution: 1.97 Å
AuthorsMarkovic-Housley, Z. / Degano, M. / Lamba, D. / von Roepenack-Lahaye, E. / Clemens, S. / Susani, M. / Ferreira, F. / Scheiner, O. / Breiteneder, H.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of a Hypoallergenic Isoform of the Major Birch Pollen Allergen Bet v 1 and its Likely Biological Function as a Plant Steroid Carrier
Authors: Markovic-Housley, Z. / Degano, M. / Lamba, D. / von Roepenack-Lahaye, E. / Clemens, S. / Susani, M. / Ferreira, F. / Scheiner, O. / Breiteneder, H.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Isoforms of Bet v 1, the major birch pollen allergen, analyzed by liquid chromatography, mass spectrometry, and cDNA cloning.
Authors: Swoboda, I. / Jilek, A. / Ferreira, F. / Engel, E. / Hoffman-Sommergruber, K. / Scheiner, O. / Kraft, D. / Breiteneder, H. / Pittenauer, E. / Schmid, E. / Vicente, O. / Heberle-Bors, E. / ...Authors: Swoboda, I. / Jilek, A. / Ferreira, F. / Engel, E. / Hoffman-Sommergruber, K. / Scheiner, O. / Kraft, D. / Breiteneder, H. / Pittenauer, E. / Schmid, E. / Vicente, O. / Heberle-Bors, E. / Ahorn, H. / Breitenbach, M.
#2: Journal: Embo J. / Year: 1989
Title: The gene coding for the major birch pollen allergen Betv1, is highly homologous to a pea disease resistance response gene.
Authors: Breiteneder, H. / Pettenburger, K. / Bito, A. / Valenta, R. / Kraft, D. / Rumpold, H. / Scheiner, O. / Breitenbach, M.
History
DepositionAug 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2163
Polymers17,4311
Non-polymers7852
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.130, 57.230, 38.650
Angle α, β, γ (deg.)90.00, 91.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MAJOR POLLEN ALLERGEN BET V 1-L


Mass: 17430.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch) / Tissue: POLLEN / Plasmid: PMW 175-BET V 1L / Production host: Escherichia coli (E. coli) / References: UniProt: P43185
#2: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM sodium acetate, 20mM ammonium sulphate, 30%Peg-MME 2000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5 %(w/v)sodium deoxycholate1drop
2100 mMsodium acetate1reservoirpH4.6
320 mMammonium sulfate1reservoir
430 %(v/v)PEG2000 MME1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. all: 32201 / Num. obs: 9670 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.3 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.2
Reflection shellResolution: 1.97→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.371 / Num. unique all: 607 / % possible all: 59.6
Reflection
*PLUS
Num. measured all: 32201
Reflection shell
*PLUS
% possible obs: 59.6 % / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 1.97→28.66 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 807800.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent correction
RfactorNum. reflection% reflectionSelection details
Rfree0.24 999 10.3 %RANDOM
Rwork0.197 ---
all-9658 --
obs-9658 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.13 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å21.44 Å2
2--0.12 Å20 Å2
3---0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.97→28.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 56 96 1380
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.831.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it3.162
X-RAY DIFFRACTIONc_scangle_it4.482.5
LS refinement shellResolution: 1.97→2.09 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 114 10.3 %
Rwork0.359 991 -
obs--64.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CHOL.PARCHOL.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / σ(I): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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