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- PDB-4bkc: Crystal Structure of a unusually linked dimeric variant of Bet v 1 -

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Basic information

Entry
Database: PDB / ID: 4bkc
TitleCrystal Structure of a unusually linked dimeric variant of Bet v 1
ComponentsMAJOR POLLEN ALLERGEN BET V 1-A
KeywordsALLERGEN / DIMERISATION / POLYSULFIDE / SULFUR INCORPORATION
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-A
Similarity search - Component
Biological speciesBETULA PENDULA (European white birch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsKofler, S.G. / Brandstetter, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Stabilization of the Dimeric Birch Pollen Allergen Bet V 1 Impacts its Immunological Properties
Authors: Kofler, S.G. / Ackaert, C. / Samonig, M. / Asam, C. / Briza, P. / Horeis-Hoeck, J. / Cabrele, C. / Ferreira, F. / Duschl, A. / Huber, C. / Brandstetter, H.
History
DepositionApr 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 2.0Apr 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_proc ...entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_validate_polymer_linkage / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 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_conn
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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: MAJOR POLLEN ALLERGEN BET V 1-A


Theoretical massNumber of molelcules
Total (without water)34,9312
Polymers34,9312
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.880, 60.950, 59.720
Angle α, β, γ (deg.)90.00, 107.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17465.691 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: BOTH MONOMERS ARE LINKED VIA A POLYSULFIDE BRIDGE BETWEEN CYS5A AND CYS5B. DUE TO OCCUPANCY REASONS, THE MODIFIED CYSTEINE RESIDUES ARE INTRODUCED AS DISCRETE COMPOUNDS.
Source: (gene. exp.) BETULA PENDULA (European white birch) / Tissue: POLLEN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15494
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.86 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M NA ACETATE PH 6.5, 27 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8865
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8865 Å / Relative weight: 1
ReflectionResolution: 1.55→41.62 Å / Num. obs: 38874 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.7
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.5 / % possible all: 98

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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 4A88

4a88


Resolution: 1.73→56.97 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.534 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY THE LIGANDS INCLUDED IN THE STRUCTURE ARE CYSTEINES BOUND TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY THE LIGANDS INCLUDED IN THE STRUCTURE ARE CYSTEINES BOUND TO ADDITIONAL CYSTEINES, AND ACCORDINGLY CYSTINE LINKED VIA 4 SULFUR ATOMS. THESE LIGANDS ARE POSITIONED AT THE SAME SITE AS CYS5 AND THEREFORE CAN BE CONSIDERED AS ALTERNATIVE CONFORMATIONS. THIS IS REFLECTED BY THE OCCUPANCIES OF THE ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24672 1424 5.1 %RANDOM
Rwork0.20124 ---
obs0.20355 26644 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.962 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20.42 Å2
2--1.41 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.73→56.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 0 219 2689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.022587
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9061.9753501
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9775330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68225.714112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6915445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.055156
X-RAY DIFFRACTIONr_chiral_restr0.060.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211954
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.21333
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21726
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.2125
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4651.9282587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.9712.8523500
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.4232587
X-RAY DIFFRACTIONr_sphericity_free19.054572
X-RAY DIFFRACTIONr_sphericity_bonded5.72652680
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 109 -
Rwork0.213 1887 -
obs--98.91 %

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