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- PDB-1ezp: GLOBAL FOLD OF MALTODEXTRIN BINDING PROTEIN COMPLEXED WITH BETA-C... -

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Basic information

Entry
Database: PDB / ID: 1ezp
TitleGLOBAL FOLD OF MALTODEXTRIN BINDING PROTEIN COMPLEXED WITH BETA-CYCLODEXTRIN USING PEPTIDE ORIENTATIONS FROM DIPOLAR COUPLINGS
ComponentsMALTODEXTRIN BINDING PERIPLASMIC PROTEIN
KeywordsSUGAR BINDING PROTEIN / residual diplar couplings / deuteration / methyl labeling
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)
MethodSOLUTION NMR / simulated annealing from extended coordinates torsion angle dynamics, finish with cartesian dynamics
AuthorsMueller, G.A. / Choy, W.Y. / Yang, D. / Forman-Kay, J.D. / Venters, R.A. / Kay, L.E.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein.
Authors: Mueller, G.A. / Choy, W.Y. / Yang, D. / Forman-Kay, J.D. / Venters, R.A. / Kay, L.E.
History
DepositionMay 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / 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: MALTODEXTRIN 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_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 243structures with the lowest energy
Representative

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Components

#1: Protein MALTODEXTRIN BINDING PERIPLASMIC PROTEIN / MALTODEXTRIN BINDING PROTEIN


Mass: 40741.098 Da / Num. of mol.: 1 / Mutation: I28T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02928, UniProt: P0AEX9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C/15N-separated NOESY
1214D 15N-seperated NOESY
1313D 13C-separated NOESY
141(HM)CMCB(CMHM)-NOESY
151TROSY-based HNCO for dipolar couplings
262TROSY-based HNCO for dipolar couplings
NMR detailsText: TROSY based HNCO sequences: J.B.NMR 14:333-343(1999)

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4 mM maltodextrin binding protein U-15N,13C,2H, with 1H amide and methyl on Val, Leu, and Ile(delta1) 2mM beta-cyclodextrin, 20 mM sodium phosphate pH 7.2, 3uM NaN3, 100uM EDTA.90% H2O/10% D2O
21.4 mM maltodextrin binding protein U-15N,13C,2H, with 1H amide and methyl on Val, Leu, and Ile(delta1) 2mM beta-cyclodextrin, 20 mM sodium phosphate pH 7.2, 3uM NaN3, 100uM EDTA. ~19mg/ml pf1 bacteriophage90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.2 ambient 310 K
27.2 ambient 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionClassification
NMRPipe1.7processing
NMRView3data analysis
CNS0.5structure solution
CNS0.5refinement
RefinementMethod: simulated annealing from extended coordinates torsion angle dynamics, finish with cartesian dynamics
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 243 / Conformers submitted total number: 10

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