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- PDB-4a84: Crystal Structure of Major Birch Pollen Allergen Bet v 1 a F30V m... -

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Basic information

Entry
Database: PDB / ID: 4a84
TitleCrystal Structure of Major Birch Pollen Allergen Bet v 1 a F30V mutant in complex with deoxycholate.
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
Major pollen allergen Bet v 1-A
Similarity search - Component
Biological speciesBETULA PENDULA (European white birch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.2Dec 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_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)18,4135
Polymers17,4141
Non-polymers9994
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.560, 55.980, 37.970
Angle α, β, γ (deg.)90.00, 93.69, 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: 17413.551 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-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#3: 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
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 31 TO VAL
Sequence detailsTHE UNIPROT SEQUENCE IS FURTHER PROCESSED INTO A MATURE FORM. MATURE PROTEIN LOST ITS STARTING METHIONINE.

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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: 37.71 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91841
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.5→32.49 Å / Num. obs: 21271 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / % possible all: 96

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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: 1.5→37.89 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.46 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24315 1069 5 %RANDOM
Rwork0.16497 ---
obs0.16907 20173 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.065 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20.23 Å2
2---0.09 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 69 188 1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021373
X-RAY DIFFRACTIONr_bond_other_d0.0010.02933
X-RAY DIFFRACTIONr_angle_refined_deg1.8462.0321888
X-RAY DIFFRACTIONr_angle_other_deg0.96432324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18425.71456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09815229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg35.442153
X-RAY DIFFRACTIONr_chiral_restr0.1020.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02242
X-RAY DIFFRACTIONr_nbd_refined0.2490.2395
X-RAY DIFFRACTIONr_nbd_other0.1940.2948
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2661
X-RAY DIFFRACTIONr_nbtor_other0.0880.2681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.271
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.8551.4831373
X-RAY DIFFRACTIONr_mcbond_other5.6911.474933
X-RAY DIFFRACTIONr_mcangle_it13.5452.1821881
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it17.5414.405461
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it20.6618.2451127
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.47932306
X-RAY DIFFRACTIONr_sphericity_free40.251568
X-RAY DIFFRACTIONr_sphericity_bonded11.81552389
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 65 -
Rwork0.259 1483 -
obs--96.21 %

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