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- PDB-4z3l: CRYSTAL STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1 MUTANT G26L, D... -

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Basic information

Entry
Database: PDB / ID: 4z3l
TitleCRYSTAL STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1 MUTANT G26L, D69I, P90L, K97I
ComponentsMajor pollen allergen Bet v 1-A
KeywordsALLERGEN / Fold Stability
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 / 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: 2.5 Å
AuthorsFreier, R. / Brandstetter, H.
CitationJournal: J.Allergy Clin.Immunol. / Year: 2016
Title: Fold stability during endolysosomal acidification is a key factor for allergenicity and immunogenicity of the major birch pollen allergen.
Authors: Machado, Y. / Freier, R. / Scheiblhofer, S. / Thalhamer, T. / Mayr, M. / Briza, P. / Grutsch, S. / Ahammer, L. / Fuchs, J.E. / Wallnoefer, H.G. / Isakovic, A. / Kohlbauer, V. / Hinterholzer, ...Authors: Machado, Y. / Freier, R. / Scheiblhofer, S. / Thalhamer, T. / Mayr, M. / Briza, P. / Grutsch, S. / Ahammer, L. / Fuchs, J.E. / Wallnoefer, H.G. / Isakovic, A. / Kohlbauer, V. / Hinterholzer, A. / Steiner, M. / Danzer, M. / Horejs-Hoeck, J. / Ferreira, F. / Liedl, K.R. / Tollinger, M. / Lackner, P. / Johnson, C.M. / Brandstetter, H. / Thalhamer, J. / Weiss, R.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: Major pollen allergen Bet v 1-A
C: Major pollen allergen Bet v 1-A
E: Major pollen allergen Bet v 1-A
F: Major pollen allergen Bet v 1-A
D: Major pollen allergen Bet v 1-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,44020
Polymers105,0956
Non-polymers1,34514
Water3,963220
1
A: Major pollen allergen Bet v 1-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8044
Polymers17,5161
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Major pollen allergen Bet v 1-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9005
Polymers17,5161
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Major pollen allergen Bet v 1-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6122
Polymers17,5161
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Major pollen allergen Bet v 1-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6122
Polymers17,5161
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Major pollen allergen Bet v 1-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9966
Polymers17,5161
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: Major pollen allergen Bet v 1-A


Theoretical massNumber of molelcules
Total (without water)17,5161
Polymers17,5161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.290, 143.340, 148.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11E-201-

SO4

21C-318-

HOH

31F-331-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23E
14A
24F
15A
25D
16B
26C
17B
27E
18B
28F
19B
29D
110C
210E
111C
211F
112C
212D
113E
213F
114E
214D
115F
215D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 1 - 159 / Label seq-ID: 1 - 159

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23ED
14AA
24FE
15AA
25DF
16BB
26CC
17BB
27ED
18BB
28FE
19BB
29DF
110CC
210ED
111CC
211FE
112CC
212DF
113ED
213FE
114ED
214DF
115FE
215DF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 17515.789 Da / Num. of mol.: 6 / Mutation: G26L D69I P90L K97I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch) / Gene: BETVIA, BETVI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15494
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 25% PEG8000, 0.2 M lithium sulfate, 0.1 M HEPES pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.5→37.02 Å / Num. all: 184278 / Num. obs: 45112 / % possible obs: 99.7 % / Redundancy: 3.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.148 / Net I/σ(I): 5.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.6 / Num. measured obs: 14689 / Num. unique all: 4358 / CC1/2: 0.576 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A88

4a88


Resolution: 2.5→37.02 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.2555 / WRfactor Rwork: 0.2122 / FOM work R set: 0.8379 / SU B: 8.575 / SU ML: 0.192 / SU R Cruickshank DPI: 0.4382 / SU Rfree: 0.2771 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.438 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 2334 5.2 %RANDOM
Rwork0.2122 ---
obs0.2144 42773 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.31 Å2 / Biso mean: 29.984 Å2 / Biso min: 7.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0 Å2
2--1.06 Å2-0 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 2.5→37.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7418 0 70 220 7708
Biso mean--73.93 29.15 -
Num. residues----954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0197670
X-RAY DIFFRACTIONr_angle_refined_deg2.3411.97710401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7825960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88925.419334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.221151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.5731518
X-RAY DIFFRACTIONr_chiral_restr0.150.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215733
X-RAY DIFFRACTIONr_mcbond_it2.2952.7623822
X-RAY DIFFRACTIONr_mcangle_it3.6074.1344770
X-RAY DIFFRACTIONr_scbond_it3.6953.1583845
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A1980.14
12B1980.14
21A2000.15
22C2000.15
31A1910.12
32E1910.12
41A1900.15
42F1900.15
51A1930.15
52D1930.15
61B2040.12
62C2040.12
71B1890.12
72E1890.12
81B1930.12
82F1930.12
91B1920.13
92D1920.13
101C1920.15
102E1920.15
111C2020.16
112F2020.16
121C2050.12
122D2050.12
131E1890.11
132F1890.11
141E1890.15
142D1890.15
151F1850.15
152D1850.15
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 180 -
Rwork0.283 3114 -
all-3294 -
obs--99.76 %

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