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- PDB-4a8g: Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in com... -

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Basic information

Entry
Database: PDB / ID: 4a8g
TitleCrystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with dimethylbenzylammonium propane sulfonate
ComponentsMAJOR POLLEN ALLERGEN BET V 1-A
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
3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE / Major pollen allergen Bet v 1-A
Similarity search - Component
Biological speciesBETULA PENDULA (European white birch)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 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-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0075
Polymers17,4621
Non-polymers5464
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.720, 55.690, 38.030
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17461.594 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: P15494
#2: Chemical ChemComp-DMX / 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE


Mass: 257.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO3S
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 120 / 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.

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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: 37.85 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 28, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→37.97 Å / Num. obs: 7052 / % possible obs: 87.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 8 / % possible all: 93.7

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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 4A80

4a80


Resolution: 2.1→37.97 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.888 / SU B: 6.036 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.436 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24906 331 4.7 %RANDOM
Rwork0.16254 ---
obs0.1667 6705 87.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.549 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.17 Å2
2--0.17 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 32 120 1384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021338
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9871821
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58125.61457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36315230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.233153
X-RAY DIFFRACTIONr_chiral_restr0.1010.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211006
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2669
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2868
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9161.5804
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69721299
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7763502
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5284.5470
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 28 -
Rwork0.155 510 -
obs--92.28 %

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