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- PDB-1qmr: BIRCH POLLEN ALLERGEN BET V 1 MUTANT N28T, K32Q, E45S, P108G -

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Basic information

Entry
Database: PDB / ID: 1qmr
TitleBIRCH POLLEN ALLERGEN BET V 1 MUTANT N28T, K32Q, E45S, P108G
ComponentsMAJOR POLLEN ALLERGEN BET V 1-A
KeywordsALLERGEN / PATHOGENESIS-RELATED PROTEIN
Function / homology
Function and homology information


response to biotic stimulus / 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 VERRUCOSA (European white birch)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHenriksen, A. / Holm, J.O. / Spangfort, M.D. / Gajhede, M.
Citation
Journal: J Immunol. / Year: 2004
Title: Allergy vaccine engineering: epitope modulation of recombinant Bet v 1 reduces IgE binding but retains protein folding pattern for induction of protective blocking-antibody responses.
Authors: Holm, J. / Gajhede, M. / Ferreras, M. / Henriksen, A. / Ipsen, H. / Larsen, J.N. / Lund, L. / Jacobi, H. / Millner, A. / Wurtzen, P.A. / Spangfort, M.D.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: X-Ray and NMR Structure of Bet V 1, the Origin of Birch Pollen Allergy
Authors: Gajhede, M. / Osmark, P. / Poulsen, F.M. / Ipsen, H. / Larsen, J.N. / Van Neerven, R.J.J. / Schou, C. / Lowenstein, H. / Spangfort, M.D.
History
DepositionOct 6, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.status_code_sf
Revision 1.5Dec 13, 2023Group: 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
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: MAJOR POLLEN ALLERGEN BET V 1-A


Theoretical massNumber of molelcules
Total (without water)17,3311
Polymers17,3311
Non-polymers00
Water82946
1
A: MAJOR POLLEN ALLERGEN BET V 1-A

A: MAJOR POLLEN ALLERGEN BET V 1-A


Theoretical massNumber of molelcules
Total (without water)34,6632
Polymers34,6632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)32.347, 74.196, 119.548
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 MAJOR POLLEN ALLERGEN BET V 1-A / BET V 1


Mass: 17331.428 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BETULA VERRUCOSA (European white birch)
Cell: POLLEN / Cellular location: CYTOPLASM / Gene: BET V 1 1.2801 / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P15494
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION ASN28THR, LYS32GLN, GLU45SER, PRO108GLY
Sequence detailsTHE LEU 62 SWS P15494 PHE 62 CONFLICT IS A KNOWN VARIANT FROM THE SWISSPROT SEQUENCE TAKEN FROM ...THE LEU 62 SWS P15494 PHE 62 CONFLICT IS A KNOWN VARIANT FROM THE SWISSPROT SEQUENCE TAKEN FROM REFERENCE: BREITENEDER H.,PETTENBURGER K.,BITO A.,VALENTA R., KRAFT D.,RUMPOLD H.,SCHEINER O.,BREITENBACH M. EMBO J. 8:1935-1938(1989).

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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: 40.56 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
32.2 Mammonium sulfate1reservoir
4100 mMsodium citrate1reservoir
51 %dioxane1reservoir
60.01 %sodium azide1reservoir
1reservoir1drop
2rBet v 1 mutant1dropdialyzed against 10 mM Tris-HCl

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→37 Å / Num. obs: 7832 / % possible obs: 96.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 11.4 Å2 / Rsym value: 0.04 / Net I/σ(I): 34
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 9.5 / Rsym value: 0.135 / % possible all: 78.5
Reflection
*PLUS
Num. measured all: 55800 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 78.5 % / Rmerge(I) obs: 0.165

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BV1

1bv1


Resolution: 2.15→30 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 248643.49 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 407 5.2 %RANDOM
Rwork0.196 ---
obs0.196 7797 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.7618 Å2 / ksol: 0.330851 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---4.5 Å20 Å2
3---4.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 0 46 1269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 56 5.4 %
Rwork0.203 981 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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