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- PDB-1a7l: DOMINANT B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRU... -

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Basic information

Entry
Database: PDB / ID: 1a7l
TitleDOMINANT B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRUS IN THE FORM OF AN INSERTED PEPTIDE SEGMENT IN MALTODEXTRIN-BINDING PROTEIN
ComponentsMALE-B363
KeywordsTRANSPORT / PRES2 / EPITOPE / HEPATITIS B / MALTOSE-BINDING PROTEIN
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 speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSaul, F.A. / Vulliez-Lenormand, B. / Lema, F. / Bentley, G.A.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of a dominant B-cell epitope from the preS2 region of hepatitis B virus in the form of an inserted peptide segment in maltodextrin-binding protein.
Authors: Saul, F.A. / Vulliez-le Normand, B. / Lema, F. / Bentley, G.A.
#1: Journal: Protein Eng. / Year: 1997
Title: Maltodextrin-Binding Protein Hybrids Carrying Epitopes from the Pres2 Region of Hepatitis B Virus: Expression, Antibody-Binding and Preliminary Crystallographic Studies
Authors: Vulliez-Le Normand, B. / Saul, F.A. / Martineau, P. / Lema, F. / Hofnung, M. / Bentley, G.A.
History
DepositionMar 16, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_conn / 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 / _atom_site.type_symbol / _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_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALE-B363
B: MALE-B363
C: MALE-B363
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9776
Polymers127,9513
Non-polymers1,0273
Water86548
1
A: MALE-B363
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9922
Polymers42,6501
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MALE-B363
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9922
Polymers42,6501
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MALE-B363
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9922
Polymers42,6501
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: MALE-B363
hetero molecules

B: MALE-B363
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9854
Polymers85,3002
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area4350 Å2
ΔGint-16 kcal/mol
Surface area28900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.600, 71.300, 123.200
Angle α, β, γ (deg.)90.00, 94.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.73069, 0.634786, -0.251274), (-0.631036, 0.76844, 0.106271), (0.260548, 0.080911, 0.962064)-28.9222, -8.4477, -8.5446
2given(0.887602, 0.188515, -0.420268), (0.172008, 0.710748, 0.682092), (0.42729, -0.677716, 0.598435)25.051, -66.3384, 4.4872
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS THREE INDEPENDENT MOLECULES OF MALE-B363. EACH IS ASSOCIATED WITH A BOUND MOLECULE OF MALTOSE SUBSTRATE. THE FOLLOWING CHAIN IDENTIFIERS ARE USED: CHAIN A, MALE-B363 MOLECULE 1; CHAIN B, MALE-B363 MOLECULE 2; CHAIN C, MALE-B363 MOLECULE 3; CHAIN D, HET GROUP ASSOCIATED WITH MOLECULE 1; CHAIN E, HET GROUP ASSOCIATED WITH MOLECULE 2; CHAIN F, HET GROUP ASSOCIATED WITH MOLECULE 3; CHAIN X, SOLVENTS ASSOCIATED WITH MOLECULE 1; CHAIN Y, SOLVENTS ASSOCIATED WITH MOLECULE 2; CHAIN Z, SOLVENTS ASSOCIATED WITH MOLECULE 3.

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Components

#1: Protein MALE-B363


Mass: 42650.176 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Strain: ED9 / Gene: MBP MUTANT / Plasmid: PPD91-(DERIVATIVE) / Gene (production host): MBP MUTANT / 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.: 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
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMALE-B363 IS AN INSERTION/DELETION MUTANT OF THE E. COLI MALTODEXTRIN-BINDING PROTEIN (MBP) ...MALE-B363 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 SURFACE ANTIGEN. AMINO ACIDS BELONGING TO THE PRES2 EPITOPE ARE DESIGNATED 132E TO 145E (POSITIONS 132-145 OF THE VIRAL SURFACE ANTIGEN). RESIDUES DESIGNATED 364I, 365I, AND 380I-389I, WHICH FLANK THE EPITOPE SEGMENT, RESULT FROM THE GENETIC CONSTRUCTION USED TO PERMIT THE INSERTION. NUMBERING OF THE INSERTED SEQUENCE IS THUS 364I, 365I, 132E TO 145E, AND 380I TO 389I. THESE RESIDUES REPLACE WILD-TYPE MBP RESIDUES FROM POSITIONS 364 - 370. THE NUMBERING OF MBP RESIDUES IN THIS ENTRY CORRESPONDS TO THE SEQUENCE POSITIONS OF WILD-TYPE MBP.

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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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growpH: 8.5
Details: PROTEIN CONCENTRATION 3.0MG/ML, BUFFER 0.1M TRIS-HCL PH 8.5 WITH 0.2 M MGCL2, 1 MM MALTOSE, 26% PEG 4000.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Vulliez-Le Normand, B., (1997) Protein Eng., 10, 175.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.0 mg/mlprotein1drop
226 %PEG40001reservoir
30.1 MTris-HCl1reservoir
41 mMmaltose1reservoir
50.2 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. obs: 24492 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 14.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.7 / % possible all: 90
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 15 Å / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.6 %
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 90 % / Redundancy: 3 % / Num. unique obs: 2146 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
XDSdata reduction
MARSCALEdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MBP RESIDUES 4 - 362 (PDB ENTRY 1ANF)

1anf


Resolution: 2.9→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.286 592 2.5 %RANDOM
Rwork0.192 ---
obs0.192 23877 98 %-
Displacement parametersBiso mean: 26.9 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8637 0 69 48 8754
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.183
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.15
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.9→3.03 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.357 89 2.96 %
Rwork0.248 2658 -
obs--91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.MALTOPOL.MAL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.15
LS refinement shell
*PLUS
Rfactor Rfree: 0.357 / Rfactor Rwork: 0.248

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