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- PDB-4bk7: Crystal Structure of a variant of the Major Birch Pollen Allergen... -

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Basic information

Entry
Database: PDB / ID: 4bk7
TitleCrystal Structure of a variant of the Major Birch Pollen Allergen Bet v 1
ComponentsMAJOR POLLEN ALLERGEN BET V 1-A
KeywordsALLERGEN / PR-10
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: 1.14 Å
AuthorsKofler, S. / 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 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _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

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Assembly

Deposited unit
A: MAJOR POLLEN ALLERGEN BET V 1-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,30310
Polymers17,4461
Non-polymers8589
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.732, 55.811, 38.099
Angle α, β, γ (deg.)90.00, 93.25, 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


Mass: 17445.594 Da / Num. of mol.: 1 / Mutation: YES
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: P15494
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE UNIPROT SEQUENCE IS FURTHER PROCESSED INTO A MATURE FORM. STARTING METHIONINE OF MATURE PROTEIN ...THE UNIPROT SEQUENCE IS FURTHER PROCESSED INTO A MATURE FORM. STARTING METHIONINE OF MATURE PROTEIN IS CLEAVED. TYROSINE 5 TO PHENYLALANINE EXCHANGE

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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: 1.99 Å3/Da / Density % sol: 38.08 % / Description: NONE
Crystal growpH: 4.5 / Details: 2M AMMONIUM SULFATE, 1.5 % MPD, pH 4.5

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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: Sep 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8865 Å / Relative weight: 1
ReflectionResolution: 1.14→55.81 Å / Num. obs: 47976 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.1
Reflection shellResolution: 1.14→1.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.5 / % possible all: 80.7

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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: 1.14→38.04 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.05 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17545 2439 5.1 %RANDOM
Rwork0.13446 ---
obs0.13656 45515 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.367 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.1 Å2
2--0.31 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.14→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 50 159 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191488
X-RAY DIFFRACTIONr_bond_other_d0.0020.02981
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.992045
X-RAY DIFFRACTIONr_angle_other_deg0.86332429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59426.09464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4415250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg33.604153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
X-RAY DIFFRACTIONr_nbd_refined0.3080.2442
X-RAY DIFFRACTIONr_nbd_other0.1970.2916
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2682
X-RAY DIFFRACTIONr_nbtor_other0.0880.2709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2130.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3490.289
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.931.2251488
X-RAY DIFFRACTIONr_mcbond_other3.7931.222981
X-RAY DIFFRACTIONr_mcangle_it10.4741.8042043
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.6991.8242429
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_restr2.73132469
X-RAY DIFFRACTIONr_sphericity_free23.978541
X-RAY DIFFRACTIONr_sphericity_bonded8.90552552
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 131 -
Rwork0.194 2569 -
obs--74.11 %

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