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- PDB-3mbp: MALTODEXTRIN-BINDING PROTEIN WITH BOUND MALTOTRIOSE -

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Basic information

Entry
Database: PDB / ID: 3mbp
TitleMALTODEXTRIN-BINDING PROTEIN WITH BOUND MALTOTRIOSE
ComponentsMALTODEXTRIN-BINDING PROTEIN
KeywordsPERIPLASMIC 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-maltotriose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH 2MBP / Resolution: 1.7 Å
AuthorsSpurlino, J.C. / Quiocho, F.A.
Citation
Journal: Structure / Year: 1997
Title: Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor.
Authors: Quiocho, F.A. / Spurlino, J.C. / Rodseth, L.E.
#1: Journal: Biochemistry / Year: 1993
Title: Refined 1.8-A Structure Reveals the Mode of Binding of Beta-Cyclodextrin to the Maltodextrin Binding Protein
Authors: Sharff, A.J. / Rodseth, L.E. / Quiocho, F.A.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Atomic Interactions in Protein-Carbohydrate Complexes. Tryptophan Residues in the Periplasmic Maltodextrin Receptor for Active Transport and Chemotaxis
Authors: Spurlino, J.C. / Rodseth, L.E. / Quiocho, F.A.
#3: Journal: Biochemistry / Year: 1992
Title: Crystallographic Evidence of a Large Ligand-Induced Hinge-Twist Motion between the Two Domains of the Maltodextrin Binding Protein Involved in Active Transport and Chemotaxis
Authors: Sharff, A.J. / Rodseth, L.E. / Spurlino, J.C. / Quiocho, F.A.
#4: Journal: J.Biol.Chem. / Year: 1991
Title: The 2.3-A Resolution Structure of the Maltose-or Maltodextrin-Binding Protein, a Primary Receptor of Bacterial Active Transport and Chemotaxis
Authors: Spurlino, J.C. / Lu, G.Y. / Quiocho, F.A.
History
DepositionJun 25, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALTODEXTRIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2582
Polymers40,7531
Non-polymers5041
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.070, 68.430, 57.940
Angle α, β, γ (deg.)90.00, 112.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MALTODEXTRIN-BINDING PROTEIN


Mass: 40753.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: PERIPLASM / Gene: MALE / References: UniProt: P02928, 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 genetically manipulated 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.77 Å3/Da / Density % sol: 49 %
Crystal growpH: 6.2
Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8000, 10 MM CITRATE, PH 6.2
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlMBP1drop
21 mMmaltodextrin1drop
316 %(w/v)PEG60001drop
422 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 1, 1989 / Details: NA
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. obs: 39297 / % possible obs: 86 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.0969 / Net I/σ(I): 13.88
Reflection shellResolution: 1.7→1.82 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.244 / % possible all: 46
Reflection shell
*PLUS
% possible obs: 46 %

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Processing

Software
NameVersionClassification
PROTEINmodel building
CHAINmodel building
PROLSQrefinement
SDMSDETECTOR SYSTEM (NIELSEN)data reduction
SDMSDETECTOR SYSTEM (NIELSEN)data scaling
PROTEINphasing
CHAINphasing
RefinementMethod to determine structure: ISOMORPHOUS WITH 2MBP
Starting model: PDB ENTRY 2MBP

2mbp
PDB Unreleased entry


Resolution: 1.7→10 Å / σ(F): 2 / Details: X-PLOR ALSO WAS USED.
RfactorNum. reflection% reflection
Rwork0.164 --
obs-29814 75 %
Displacement parametersBiso mean: 27.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2878 0 34 244 3156
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0270.02
X-RAY DIFFRACTIONp_angle_d0.0530.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0650.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.0271
X-RAY DIFFRACTIONp_mcangle_it1.8141.5
X-RAY DIFFRACTIONp_scbond_it2.9472
X-RAY DIFFRACTIONp_scangle_it4.0582.5
X-RAY DIFFRACTIONp_plane_restr0.0140.015
X-RAY DIFFRACTIONp_chiral_restr0.1540.1
X-RAY DIFFRACTIONp_singtor_nbd0.1970.5
X-RAY DIFFRACTIONp_multtor_nbd0.2240.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2150.5
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor22.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS

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