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- PDB-1iud: MALTODEXTRIN-BINDING PROTEIN INSERTION/DELETION MUTANT WITH AN IN... -

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Basic information

Entry
Database: PDB / ID: 1iud
TitleMALTODEXTRIN-BINDING PROTEIN INSERTION/DELETION MUTANT WITH AN INSERTED B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRUS
ComponentsMALTODEXTRIN-BINDING PROTEIN MALE-B133
KeywordsHYBRID PROTEIN / PRES2 EPITOPE ANTIGEN VIRUS / VIRAL EPITOPE INSERTION / SUGAR TRANSPORT
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
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 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSaul, F.A. / Vulliez-Le Normand, B. / Lema, F. / Bentley, G.A.
CitationJournal: Proteins / Year: 1997
Title: Crystal structure of a recombinant form of the maltodextrin-binding protein carrying an inserted sequence of a B-cell epitope from the preS2 region of hepatitis B virus.
Authors: Saul, F.A. / Vulliez-le Normand, B. / Lema, F. / Bentley, G.A.
History
DepositionMay 29, 1996Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / 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_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.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.process_site / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALTODEXTRIN-BINDING PROTEIN MALE-B133
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1492
Polymers41,8071
Non-polymers3421
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.100, 97.400, 137.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MALTODEXTRIN-BINDING PROTEIN MALE-B133


Mass: 41807.199 Da / Num. of mol.: 1
Mutation: INSERTED B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MALE-B133 / Plasmid: PD1 / Gene (production host): MALE-B133 / Production host: Escherichia coli (E. coli) / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
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
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMALE-B133 IS AN INSERTION/DELETION MUTANT OF THE E. COLI MALTODEXTRIN-BINDING PROTEIN (MBP) ...MALE-B133 IS AN INSERTION/DELETION MUTANT OF THE E. COLI MALTODEXTRIN-BINDING PROTEIN (MBP) CARRYING THE AMINO-ACID SEQUENCE OF A B-CELL EPITOPE FROM THE PRES2 REGION OF THE HEPATITIS B VIRUS (HBV) ENVELOPE PROTEIN. THE AMINO ACIDS BELONGING TO THE PRES2 EPITOPE ARE DESIGNATED 132E TO 145E (POSITIONS 132 TO 145 OF THE VIRAL ENVELOPE PROTEIN). RESIDUES DESIGNATED 130I, 131I, 146I, 147I AND 148I, WHICH FLANK THE PRES2 EPITOPE, RESULT FROM THE CREATION OF A BAMHI RESTRICTION SITE PERMITTING THE INSERTION. THE COMPLETE INSERTED SEQUENCE IS THUS 130I, 131I, 132E - 145E, 146I, 147I, AND 148I. THESE 19 RESIDUES REPLACE WILD-TYPE MBP RESIDUES FROM POSITIONS 134 TO 142 (DELETED IN THE HYBRID PROTEIN). THE INSERTION/DELETION MUTATION RESULTS IN A NET GAIN OF 10 AMINO ACIDS IN THE RECOMBINANT PROTEIN. THE NUMBERING OF MBP RESIDUES IN THIS ENTRY CORRESPONDS TO THE SEQUENCE POSITIONS OF WILD-TYPE MBP. NO INTERPRETED ELECTRON DENSITY WAS FOUND FOR MBP RESIDUES 1, 2, 3, 143, AND FOR INSERTED RESIDUES 141E TO 148I.

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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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 %PEG60001dropcan be replaced by PEG8000
210 mMTris-HCl1drop
3100 mM1dropNaCl
43 mM1dropNaN3
51 mMmaltose1drop
63 mg/mlprotein1drop
722 %PEG1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 11201 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.1 / % possible all: 97
Reflection shell
*PLUS
% possible obs: 97 % / Num. unique obs: 1108

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE MALTOSE-BINDING PROTEIN

Resolution: 2.7→6 Å / σ(F): 2
Details: RESIDUES GLU 171 - GLY 174 HAVE WEAK ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.281 -5 %
Rwork0.178 --
obs0.178 9349 89 %
Displacement parametersBiso mean: 34 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 23 8 2902
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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