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- PDB-2d21: NMR Structure of stereo-array isotope labelled (SAIL) maltodextri... -

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Basic information

Entry
Database: PDB / ID: 2d21
TitleNMR Structure of stereo-array isotope labelled (SAIL) maltodextrin-binding protein (MBP)
ComponentsMaltose-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN / stereo-array isotope labelling / SAIL
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKainosho, M. / Torizawa, T. / Iwashita, Y. / Terauchi, T. / Ono, A.M. / Guntert, P.
CitationJournal: Nature / Year: 2006
Title: Optimal isotope labelling for NMR protein structure determinations.
Authors: Kainosho, M. / Torizawa, T. / Iwashita, Y. / Terauchi, T. / Mei Ono, A. / Guntert, P.
History
DepositionSep 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 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: Maltose-binding periplasmic protein


Theoretical massNumber of molelcules
Total (without water)40,7531
Polymers40,7531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Maltose-binding periplasmic protein / Maltodextrin-binding protein / MMBP / MBP


Mass: 40753.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: cell-free protein synthesis / References: UniProt: P0AEX9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D NOESY

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Sample preparation

DetailsContents: 0.33mM SAIL-MBP, 3.3mM beta-cyclodextrin, 20mM sodium phosphate, 3mM NaN3, CompleteMini protease inhibitor mix
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM sodium phosphate / pH: 7.2 / Pressure: AMBIENT / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
OPALp1.4R.Koradi,M.Billeter,P.Guntertrefinement
CYANA2.1P.Guntert et al.structure solution
Sparky3.11T.D.Goddard,D.G.Knellerdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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