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- PDB-2klf: PERE NMR structure of maltodextrin-binding protein -

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Basic information

Entry
Database: PDB / ID: 2klf
TitlePERE NMR structure of maltodextrin-binding protein
ComponentsMaltose-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / maltose-binding protein / paramagnetic relaxation / Gd(DTPA-BMA) / Sugar transport / 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
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, Paramagnetic environment relaxation enhancement refinement
Model detailsclosest to the average, model 3
AuthorsMadl, T. / Bermel, W. / Zangger, K.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Use of Relaxation Enhancements in a Paramagnetic Environment for the Structure Determination of Proteins Using NMR Spectroscopy
Authors: Madl, T. / Bermel, W. / Zangger, K.
History
DepositionJul 2, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)40,7411
Polymers40,7411
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 40741.098 Da / Num. of mol.: 1 / Mutation: I2T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4034, JW3994, malE / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D 1H-15N HSQC
131CON
141COCA

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Sample preparation

DetailsContents: 20mM potassium phosphate-1, 2mM beta-cyclodextrin-2, 3mM sodium azide-3, 100mM EDTA-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMpotassium phosphate-11
2 mMbeta-cyclodextrin-21
3 mMsodium azide-31
100 mMEDTA-41
Sample conditionsIonic strength: 0.02 / pH: 7.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, Paramagnetic environment relaxation enhancement refinement
Software ordinal: 1
Details: PERE restraints were incorporated using lab-written scripts
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 3

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