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- PDB-4b9r: Crystal structure of the Major Birch Pollen Allergen Bet v 1.0101... -

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Basic information

Entry
Database: PDB / ID: 4b9r
TitleCrystal structure of the Major Birch Pollen Allergen Bet v 1.0101 (isoform a) nitrated in vitro with tetranitromethan.
ComponentsMAJOR POLLEN ALLERGEN BET V 1-A
KeywordsALLERGEN / NITRATION / NITROTYROSINE
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsKofler, S. / Ackaert, C. / Brandstetter, H.
CitationJournal: Plos One / Year: 2014
Title: The Impact of Nitration on the Structure and Immunogenicity of the Major Birch Pollen Allergen Bet V 1.0101.
Authors: Ackaert, C. / Kofler, S. / Horejs-Hoeck, J. / Zulehner, N. / Asam, C. / Von Grafenstein, S. / Fuchs, J.E. / Briza, P. / Liedl, K.R. / Bohle, B. / Ferreira, F. / Brandstetter, H. / Oostingh, G.J. / Duschl, A.
History
DepositionSep 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 27, 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 / 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 / _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_comp_id / _struct_conn.ptnr1_auth_seq_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,7382
Polymers17,6421
Non-polymers961
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.410, 55.140, 37.610
Angle α, β, γ (deg.)90.00, 92.77, 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: 17641.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NITRATION OF TYR5,66,83 AND 150 TO META-NITRO-TYROSINE (NIY)
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL METHIONINE PROCESSED, TYROSINES 5 66 83 AND 150 NITRATED

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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: 1.92 Å3/Da / Density % sol: 35.9 % / Description: NONE
Crystal growpH: 7
Details: 2M AMMONIUM SULFATE 1.5% 2-METHYL-2,4-PENTANDIOL, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9737
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 1.76→37.57 Å / Num. obs: 12627 / % possible obs: 95.9 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / % possible all: 92.3

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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 4A8U

4a8u


Resolution: 1.76→37.57 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.483 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 124-126 DISORDERED AND THEIR SIDE CHAINS HAVE BEEN DELETED
RfactorNum. reflection% reflectionSelection details
Rfree0.24913 625 5 %RANDOM
Rwork0.16418 ---
obs0.16824 11984 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20.07 Å2
2---0.31 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.76→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 5 104 1339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021297
X-RAY DIFFRACTIONr_bond_other_d0.0020.02876
X-RAY DIFFRACTIONr_angle_refined_deg1.2812.0291752
X-RAY DIFFRACTIONr_angle_other_deg0.86132127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.215158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3126.03853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85315211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.387153
X-RAY DIFFRACTIONr_chiral_restr0.0650.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_nbd_refined0.3910.2353
X-RAY DIFFRACTIONr_nbd_other0.2380.2932
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2608
X-RAY DIFFRACTIONr_nbtor_other0.0870.2633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.243
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.6952.2411297
X-RAY DIFFRACTIONr_mcbond_other1483.873.347876
X-RAY DIFFRACTIONr_mcangle_it10.1043.3191750
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_restr1.59632159
X-RAY DIFFRACTIONr_sphericity_free35.496536
X-RAY DIFFRACTIONr_sphericity_bonded9.32152206
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 41 -
Rwork0.21 784 -
obs--86.03 %

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