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- PDB-3ob4: MBP-fusion protein of the major peanut allergen Ara h 2 -

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Basic information

Entry
Database: PDB / ID: 3ob4
TitleMBP-fusion protein of the major peanut allergen Ara h 2
ComponentsMaltose ABC transporter periplasmic protein,Arah 2
KeywordsALLERGEN / Alpha-Amylase Inhibitors (AAI) / Lipid Transfer (LT) and Seed Storage (SS) Protein family / seed storage protein / fusion protein / chimera protein
Function / homology
Function and homology information


nutrient reservoir activity / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...nutrient reservoir activity / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane / metal ion binding
Similarity search - Function
Napin/ 2S seed storage protein/Conglutin / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltotriose / Ara h 2 allergen / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Arachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.706 Å
AuthorsMueller, G.A. / Gosavi, R.A. / Moon, A.F. / London, R.E. / Pedersen, L.C.
CitationJournal: Allergy / Year: 2011
Title: Ara h 2: crystal structure and IgE binding distinguish two subpopulations of peanut allergic patients by epitope diversity.
Authors: Mueller, G.A. / Gosavi, R.A. / Pomes, A. / Wunschmann, S. / Moon, A.F. / London, R.E. / Pedersen, L.C.
History
DepositionAug 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 26, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 17, 2021Group: Database references / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_name_com / entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _entity.details ..._chem_comp.pdbx_synonyms / _entity.details / _entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_mutation / _entity.src_method / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 2.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 999FUSION PROTEIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN AND ARAH2 WITH LINKER REGION NAAA. THE ...FUSION PROTEIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN AND ARAH2 WITH LINKER REGION NAAA. THE NUMBERING OF ARAH2 CORRESPONDS TO STANDARD RESIDUE NUMBERING + 1000. The sequence number for arah2 is as published in: STANLEY ET AL. IDENTIFICATION AND MUTATIONAL ANALYSIS OF THE IMMUNODOMINANT IGE BINDING EPITOPES OF THE MAJOR PEANUT ALLERGEN ARA H 2. ARCH BIOCHEM BIOPHYS. 1997 Jun 15;342(2):244-53.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose ABC transporter periplasmic protein,Arah 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,62810
Polymers55,6581
Non-polymers9709
Water1,24369
1
A: Maltose ABC transporter periplasmic protein,Arah 2
hetero molecules

A: Maltose ABC transporter periplasmic protein,Arah 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,25720
Polymers111,3172
Non-polymers1,94018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6340 Å2
ΔGint-164 kcal/mol
Surface area39970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.847, 87.381, 113.137
Angle α, β, γ (deg.)90.00, 103.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Maltose ABC transporter periplasmic protein,Arah 2


Mass: 55658.418 Da / Num. of mol.: 1
Fragment: MBP, UNP residues 27-392,arah2, UNP residues 28-158
Mutation: D82A,K83A,E172A,N173A,K239A
Source method: isolated from a genetically manipulated source
Details: chimera protein is made with surface mutations on the MBP as well as a fixed arm linker to the arah2 protein,chimera protein is made with surface mutations on the MBP as well as a fixed arm ...Details: chimera protein is made with surface mutations on the MBP as well as a fixed arm linker to the arah2 protein,chimera protein is made with surface mutations on the MBP as well as a fixed arm linker to the arah2 protein
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Arachis hypogaea (peanut)
Gene: HMPREF9530_03068, Ara h 2 / Plasmid: pMALX / Production host: Escherichia coli (E. coli) / Strain (production host): OrgamiB(DE3)
References: UniProt: D8A942, UniProt: A0A445BYI5, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFUSION PROTEIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN AND ARAH2 WITH LINKER REGION NAAA. THE ...FUSION PROTEIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN AND ARAH2 WITH LINKER REGION NAAA. THE NUMBERING OF ARAH2 CORRESPONDS TO STANDARD RESIDUE NUMBERING + 1000. The sequence number for arah2 is as published in: STANLEY ET AL. IDENTIFICATION AND MUTATIONAL ANALYSIS OF THE IMMUNODOMINANT IGE BINDING EPITOPES OF THE MAJOR PEANUT ALLERGEN ARA H 2. ARCH BIOCHEM BIOPHYS. 1997 Jun 15;342(2):244-53.

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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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium citrate 1.8M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARCCD300 / Detector: CCD / Date: Jun 18, 2010
RadiationMonochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 16353 / Num. obs: 16353 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.104 / Net I/σ(I): 7.9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 448 / Rsym value: 0.321 / % possible all: 49.6

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
PHENIX(phenix.refine: 1.4_6)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DMO

2dmo


Resolution: 2.706→44.567 Å / SU ML: 1.21 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 833 5.1 %Random
Rwork0.1832 ---
all0.1869 16353 --
obs0.1868 16333 91.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.583 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.2386 Å20 Å22.7833 Å2
2--9.4009 Å20 Å2
3----6.1624 Å2
Refinement stepCycle: LAST / Resolution: 2.706→44.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3637 0 54 69 3760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053771
X-RAY DIFFRACTIONf_angle_d0.8395118
X-RAY DIFFRACTIONf_dihedral_angle_d18.6511424
X-RAY DIFFRACTIONf_chiral_restr0.057560
X-RAY DIFFRACTIONf_plane_restr0.004673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7056-2.87510.3495910.2471701X-RAY DIFFRACTION60
2.8751-3.0970.35961460.24452494X-RAY DIFFRACTION89
3.097-3.40860.29641500.21052772X-RAY DIFFRACTION99
3.4086-3.90150.26861340.17112836X-RAY DIFFRACTION100
3.9015-4.91450.19241550.13582834X-RAY DIFFRACTION100
4.9145-44.5730.21011570.16312863X-RAY DIFFRACTION100

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