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- PDB-1fqc: CRYSTAL STRUCTURE OF MALTOTRIOTOL BOUND TO CLOSED-FORM MALTODEXTR... -

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Basic information

Entry
Database: PDB / ID: 1fqc
TitleCRYSTAL STRUCTURE OF MALTOTRIOTOL BOUND TO CLOSED-FORM MALTODEXTRIN BINDING PROTEIN
ComponentsMALTODEXTRIN-BINDING PROTEIN
KeywordsSUGAR BINDING PROTEIN / sugar-binding protein / maltotriotol
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
Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsDuan, X. / Hall, J.A. / Nikaido, H. / Quiocho, F.A.
CitationJournal: J Mol Biol / Year: 2001
Title: Crystal structures of the maltodextrin/maltose-binding protein complexed with reduced oligosaccharides: flexibility of tertiary structure and ligand binding.
Authors: X Duan / J A Hall / H Nikaido / F A Quiocho /
Abstract: The structure of the maltodextrin or maltose-binding protein, an initial receptor for bacterial ABC-type active transport and chemotaxis, consists of two globular domains that are separated by a ...The structure of the maltodextrin or maltose-binding protein, an initial receptor for bacterial ABC-type active transport and chemotaxis, consists of two globular domains that are separated by a groove wherein the ligand is bound and enclosed by an inter-domain rotation. Here, we report the determination of the crystal structures of the protein complexed with reduced maltooligosaccharides (maltotriitol and maltotetraitol) in both the "closed" and "open" forms. Although these modified sugars bind to the receptor, they are not transported by the wild-type transporter. In the closed structures, the reduced sugars are buried in the groove and bound by both domains, one domain mainly by hydrogen-bonding interactions and the other domain primarily by non-polar interactions with aromatic side-chains. In the open structures, which abrogate both cellular activities of active transport and chemotaxis because of the large separation between the two domains, the sugars are bound almost exclusively to the domain rich in aromatic residues. The binding site for the open chain glucitol residue extends to a subsite that is distinct from those for the glucose residues that were uncovered in prior structural studies of the binding of active linear maltooligosaccharides. Occupation of this subsite may also account for the inability of the reduced oligosaccharides to be transported. The structures reported here, combined with those previously determined for several other complexes with active oligosaccharides in the closed form and with cyclodextrin in the open form, revealed at least four distinct modes of ligand binding but with only one being functionally active. This versatility reflects the flexibility of the protein, from very large motions of interdomain rotation to more localized side-chain conformational changes, and adaptation by the oligosaccharides as well.
History
DepositionSep 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALTODEXTRIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1992
Polymers40,6951
Non-polymers5041
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.0, 68.1, 57.5
Angle α, β, γ (deg.)90.0, 112.7, 90.0
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein MALTODEXTRIN-BINDING PROTEIN / MALTOSE-BINDING PERIPLASMIC PROTEIN / MMBP


Mass: 40695.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH MALTOTRIOTOL / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-D-glucose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[o2122h][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][<C6O5>]{[(1+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 6000, Mes, NaN3, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlMBP1drop
21 mMmaltotriitol1drop
316 %(w/v)PEG60001drop
40.02 %(w/v)sodium azide1drop
510 mMMES1drop
612 mg/mlprotein1drop
722 %PEG60001reservoir
80.02 %(w/v)sodium azide1reservoir
910 mMMES1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / % possible obs: 89.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.142 / % possible all: 73.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 170862
Reflection shell
*PLUS
% possible obs: 73.2 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.3→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.246 -random
Rwork0.199 --
obs-15811 -
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 34 120 3016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.9
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3

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