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- PDB-1bv1: BIRCH POLLEN ALLERGEN BET V 1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1bv1
TitleBIRCH POLLEN ALLERGEN BET V 1
ComponentsBET V 1
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 pendula (European white birch)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsGajhede, M. / Osmark, P. / Poulsen, F.M. / Ipsen, H. / Larson, J.N. / Joostvan, R.J. / Schou, C. / Lowenstein, H. / Spangfort, M.D.
CitationJournal: 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. / Joost van Neerven, R.J. / Schou, C. / Lowenstein, H. / Spangfort, M.D.
History
DepositionJul 8, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BET V 1


Theoretical massNumber of molelcules
Total (without water)17,4281
Polymers17,4281
Non-polymers00
Water1,51384
1
A: BET V 1

A: BET V 1


Theoretical massNumber of molelcules
Total (without water)34,8552
Polymers34,8552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)32.160, 74.240, 118.120
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 BET V 1 / MAJOR POLLEN ALLERGEN BET V 1-A


Mass: 17427.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch)
Description: COMMERCIALLY AVAILABLE POLLEN FROM ALLERGEN, SWEDEN
Cell: POLLEN / Cellular location: CYTOPLASM / Gene: BET V 1 1.2801 / Plasmid: PMALC / Cellular location (production host): CYTOPLASM / Gene (production host): MALE-BET V 1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P15494
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growpH: 6.3
Details: PROTEIN WAS CRYSTALLIZED BY MIXING 5 MG/ML PROTEIN SOLUTION WITH EQUAL AMOUNT OF 2.0 M AMS, 100 MM SODIUM CITRATE, PH 6.3
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlrecombinant Bet v 11drop
21.0 Mammonium sulfate1drop
350 mMsodium citrate1drop
40.005 %sodium azide1drop
52.0 Mammonium sulphate1reservoir
6100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 9554 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.36 / % possible all: 84.2
Reflection
*PLUS
Num. measured all: 54458
Reflection shell
*PLUS
% possible obs: 84.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2→40 Å / Rfactor Rfree error: 0.022 / Data cutoff high absF: 1000000 / Data cutoff low absF: 1.0E-5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION
RfactorNum. reflection% reflectionSelection details
Rfree0.267 986 10.4 %RANDOM
Rwork0.198 ---
obs0.198 9509 95.9 %-
Displacement parametersBiso mean: 25.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 40 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 0 84 1314
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.12
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.171.5
X-RAY DIFFRACTIONx_mcangle_it3.172
X-RAY DIFFRACTIONx_scbond_it4.52
X-RAY DIFFRACTIONx_scangle_it6.972.5
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.311 105 9.5 %
Rwork0.263 955 -
obs--78 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.12
LS refinement shell
*PLUS
Rfactor obs: 0.263

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