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- PDB-4a8u: Crystal Structure of native Birch Pollen Allergen Bet v 1 isoform j -

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Basic information

Entry
Database: PDB / ID: 4a8u
TitleCrystal Structure of native Birch Pollen Allergen Bet v 1 isoform j
ComponentsMAJOR POLLEN ALLERGEN BET V 1-J
KeywordsALLERGEN / PR-10 PROTEIN
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-J
Similarity search - Component
Biological speciesBETULA PENDULA (European white birch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsKofler, S. / Brandstetter, H.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystallographically Mapped Ligand Binding Differs in High and Low Ige Binding Isoforms of Birch Pollen Allergen Bet V 1.
Authors: Kofler, S. / Asam, C. / Eckhard, U. / Wallner, M. / Ferreira, F. / Brandstetter, H.
History
DepositionNov 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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-J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,79414
Polymers17,4311
Non-polymers1,36313
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.660, 55.690, 38.050
Angle α, β, γ (deg.)90.00, 93.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MAJOR POLLEN ALLERGEN BET V 1-J / ALLERGEN BET V I-J / ALLERGEN=BET V 1-J


Mass: 17430.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BETULA PENDULA (European white birch) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P43183

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Non-polymers , 5 types, 220 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1.97 Å3/Da / Density % sol: 37.7 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2010 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.16→18.98 Å / Num. obs: 46196 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17
Reflection shellResolution: 1.16→1.22 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 7.3 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A80

4a80


Resolution: 1.16→37.97 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.763 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.14867 2318 5 %RANDOM
Rwork0.11902 ---
obs0.12048 43861 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.03 Å2
2--0.18 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.16→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 78 207 1509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021439
X-RAY DIFFRACTIONr_bond_other_d0.0020.02950
X-RAY DIFFRACTIONr_angle_refined_deg1.5762.0151977
X-RAY DIFFRACTIONr_angle_other_deg1.09832352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9825.73861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75815242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg35.189153
X-RAY DIFFRACTIONr_chiral_restr0.1910.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211582
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02265
X-RAY DIFFRACTIONr_nbd_refined0.2490.2458
X-RAY DIFFRACTIONr_nbd_other0.1970.2932
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2653
X-RAY DIFFRACTIONr_nbtor_other0.090.2704
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.299
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.7911.1391439
X-RAY DIFFRACTIONr_mcbond_other3.3811.124950
X-RAY DIFFRACTIONr_mcangle_it9.0091.6811966
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it11.6633.211497
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it16.3886.591203
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.29332389
X-RAY DIFFRACTIONr_sphericity_free32.767539
X-RAY DIFFRACTIONr_sphericity_bonded8.99552528
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.144 124 -
Rwork0.126 2594 -
obs--80.01 %

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