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- PDB-1mdq: REFINED STRUCTURES OF TWO INSERTION(SLASH)DELETION MUTANTS PROBE ... -

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Basic information

Entry
Database: PDB / ID: 1mdq
TitleREFINED STRUCTURES OF TWO INSERTION(SLASH)DELETION MUTANTS PROBE FUNCTION OF THE MALTODEXTRIN BINDING PROTEIN
ComponentsMALTODEXTRIN BINDING PROTEIN
KeywordsSUGAR 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 / Resolution: 1.9 Å
AuthorsSharff, A.J. / Quiocho, F.A.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Refined structures of two insertion/deletion mutants probe function of the maltodextrin binding protein.
Authors: Sharff, A.J. / Rodseth, L.E. / Szmelcman, S. / Hofnung, M. / Quiocho, F.A.
#1: Journal: Biochemistry / Year: 1993
Title: Refined 1.8 Angstroms 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: 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 Transport and Chemotaxis
Authors: Sharff, A.J. / Rodseth, L.E. / Spurlino, J.C. / Quiocho, F.A.
#3: Journal: J.Biol.Chem. / Year: 1991
Title: The 2.3 Angstroms 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.
#4: Journal: J.Mol.Biol. / Year: 1987
Title: Silent and Functional Changes in the Periplasmic Maltose-Binding Protein of Escherichia Coli K12. II. Chemotaxis Towards Maltose
Authors: Duplay, P. / Szmelcman, S.
#5: Journal: J.Mol.Biol. / Year: 1987
Title: Silent and Functional Changes in the Periplasmic Maltose-Binding Protein of Escherichia Coli K12. I. Transport of Maltose
Authors: Duplay, P. / Szmelcman, S. / Bedouelle, H. / Hofnung, M.
History
DepositionAug 10, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / 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_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 / 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_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 14, 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

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Assembly

Deposited unit
A: MALTODEXTRIN BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1692
Polymers40,8261
Non-polymers3421
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.010, 66.460, 57.750
Angle α, β, γ (deg.)90.00, 113.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MALTODEXTRIN BINDING PROTEIN


Mass: 40826.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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.: 108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop
Details: reseeded into drops containing 15% PEG8000, taken from Spurlino, J.C. et al (1991). J. Biol. Chem., 266, 5202-5219.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein1drop
21 mMmaltose1drop
316 %(w/v)PEG80001drop
40.02 %sodium azide1drop
510 mMsodium citrate1drop
619 %PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 42315 / % possible obs: 78 % / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. measured all: 72712 / Rmerge(I) obs: 0.0421

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.22 -
obs0.22 23717
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 23 108 2998
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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/PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.030.033
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_planar_d0.020.011
X-RAY DIFFRACTIONp_chiral_restr0.150.16
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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