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- PDB-4a81: Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in ter... -

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Basic information

Entry
Database: PDB / ID: 4a81
TitleCrystal Structure of Major Birch Pollen Allergen Bet v 1 a in ternary complex with 8-Anilinonaphthalene-1-sulfonate (ANS) and deoxycholic acid
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
8-ANILINO-1-NAPHTHALENE SULFONATE / Major pollen allergen Bet v 1-A
Similarity search - Component
Biological speciesBETULA PENDULA (European white birch)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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 18, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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)18,3916
Polymers17,4621
Non-polymers9295
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.600, 55.820, 37.850
Angle α, β, γ (deg.)90.00, 93.04, 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-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

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Non-polymers , 6 types, 113 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#4: Chemical ChemComp-2AN / 8-ANILINO-1-NAPHTHALENE SULFONATE


Mass: 299.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13NO3S
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSTARTING METHIONINE OF UNIPROT SEQUENCE 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: 1.97 Å3/Da / Density % sol: 37.49 % / 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: Jan 19, 2011 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→37.8 Å / Num. obs: 7579 / % possible obs: 88.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 5.9 / % possible all: 90.5

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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: 2.05→37.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.985 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23011 366 4.8 %RANDOM
Rwork0.16194 ---
obs0.16525 7189 88.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.571 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.06 Å2
2--1.04 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.05→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 63 108 1397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021338
X-RAY DIFFRACTIONr_bond_other_d0.0010.02903
X-RAY DIFFRACTIONr_angle_refined_deg1.8512.0271823
X-RAY DIFFRACTIONr_angle_other_deg0.92732224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3125.78957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81715218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.126153
X-RAY DIFFRACTIONr_chiral_restr0.0940.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_nbd_refined0.2440.2372
X-RAY DIFFRACTIONr_nbd_other0.1960.2932
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2662
X-RAY DIFFRACTIONr_nbtor_other0.0940.2652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0540.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3170.245
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1680.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1351.5792
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99721281
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0853523
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8614.5507
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: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 31 -
Rwork0.151 506 -
obs--88.32 %

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