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- PDB-3h4z: Crystal Structure of an MBP-Der p 7 fusion protein -

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Basic information

Entry
Database: PDB / ID: 3h4z
TitleCrystal Structure of an MBP-Der p 7 fusion protein
ComponentsMaltose-binding periplasmic protein fused with Allergen DERP7
KeywordsALLERGEN / MBP fusion / DERP7 / Aha1/BPI domain-like / Super Roll / Sugar transport / Transport
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / 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 / extracellular region / membrane
Similarity search - Function
Bactericidal permeability-increasing protein; domain 1 - #50 / Mite allergen, group-7 / Mite allergen, group-7 superfamily / Group 7 allergen / Bactericidal permeability-increasing protein; domain 1 / Super Roll / 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 ...Bactericidal permeability-increasing protein; domain 1 - #50 / Mite allergen, group-7 / Mite allergen, group-7 superfamily / Group 7 allergen / Bactericidal permeability-increasing protein; domain 1 / Super Roll / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Mite allergen Der p 7
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Dermatophagoides pteronyssinus (European house dust mite)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPedersen, L.C. / Mueller, G.A. / London, R.E.
CitationJournal: J.Allergy Clin.Immunol. / Year: 2010
Title: The structure of the dust mite allergen Der p 7 reveals similarities to innate immune proteins.
Authors: Mueller, G.A. / Edwards, L.L. / Aloor, J.J. / Fessler, M.B. / Glesner, J. / Pomes, A. / Chapman, M.D. / London, R.E. / Pedersen, L.C.
History
DepositionApr 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein fused with Allergen DERP7
B: Maltose-binding periplasmic protein fused with Allergen DERP7
C: Maltose-binding periplasmic protein fused with Allergen DERP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,0957
Polymers187,0463
Non-polymers1,0504
Water5,801322
1
A: Maltose-binding periplasmic protein fused with Allergen DERP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7143
Polymers62,3491
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein fused with Allergen DERP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6912
Polymers62,3491
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Maltose-binding periplasmic protein fused with Allergen DERP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6912
Polymers62,3491
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)193.352, 117.904, 92.441
Angle α, β, γ (deg.)90.00, 114.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Maltose-binding periplasmic protein fused with Allergen DERP7


Mass: 62348.523 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: protein is an MBP-DERP7 fusion using a modifed pMAL vector from NEB.
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite)
Gene: malE, DERP7 / Plasmid: pMAL-x / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)PLacI / References: UniProt: P0AEX9, UniProt: P49273
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFUSION PROTEIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN AND ALLERGEN DERP7 WITH LINKER REGION ...FUSION PROTEIN OF MALTOSE-BINDING PERIPLASMIC PROTEIN AND ALLERGEN DERP7 WITH LINKER REGION AAAQTNAAA. THE NUMBERING OF DERP7 CORRESPONDS TO STANDARD RESIDUE NUMBERING + 1000

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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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 85mM Lithium sulfate, 42mM Tris pH 8.5, 12.75% PEG4K, 7.5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Feb 25, 2009 / Details: VariMax HF mirrors
RadiationMonochromator: VariMax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 76800 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 36.1 Å2 / Rsym value: 0.063 / Net I/σ(I): 28.4
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.45 / Num. unique all: 7626 / Rsym value: 0.355 / % possible all: 97.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MBP molecule from pdb id code 3dm0

3dm0


Resolution: 2.35→28.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 896959.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 3079 5.1 %RANDOM
Rwork0.249 ---
all0.251 60931 --
obs0.249 60931 77.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9992 Å2 / ksol: 0.336752 e/Å3
Displacement parametersBiso mean: 50.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å2-8.99 Å2
2--1.37 Å20 Å2
3----2.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.35→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12607 0 70 322 12999
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it9.282
X-RAY DIFFRACTIONc_scangle_it11.272.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.444 403 5.1 %
Rwork0.357 7564 -
obs--60.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cis1048.parcarbohydrate.top
X-RAY DIFFRACTION5water_rep.param

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