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- PDB-1o53: Solution structure of the N-terminal membrane anchor of E. coli e... -

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Basic information

Entry
Database: PDB / ID: 1o53
TitleSolution structure of the N-terminal membrane anchor of E. coli enzyme IIA(Glucose)
ComponentsPTS system, glucose-specific IIA component
KeywordsTRANSFERASE / amphipathic helix
Function / homology
Function and homology information


negative regulation of carbohydrate metabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / extrinsic component of cytoplasmic side of plasma membrane / kinase activity / membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Duplicated hybrid motif
Similarity search - Domain/homology
PTS system glucose-specific EIIA component / PTS system glucose-specific EIIA component
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsWang, G. / Keifer, P.A. / Peterkofsky, A.
CitationJournal: Protein Sci. / Year: 2003
Title: Solution structure of the N-terminal amphitropic domain of Escherichia coli glucose-specific enzyme IIA in membrane-mimetic micelles
Authors: Wang, G. / Keifer, P.A. / Peterkofsky, A.
History
DepositionAug 11, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionAug 19, 2003ID: 1O0Z
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: 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: PTS system, glucose-specific IIA component


Theoretical massNumber of molelcules
Total (without water)1,6971
Polymers1,6971
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 / 100No NOE violations greater than 0.20 A; rms difference for bond deviations from ideality less than 0.01 A; rms difference for angle deviations from ideality less than 2 degrees; Structures with the lowerest energies in the ensemble; Structures most resemble the average structure.
RepresentativeModel #1most resemble the average structure.

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Components

#1: Protein/peptide PTS system, glucose-specific IIA component / EIIA-GLC / Glucose-permease IIA component / Phosphotransferase enzyme II / A component / EIII-GLC


Mass: 1696.983 Da / Num. of mol.: 1
Fragment: N-terminal membrane anchor, residues 1-15 of enzyme IIA(Glucose)
Source method: obtained synthetically
Details: The peptide was synthesized using the solid-phase method and purified by HPLC. The sequence of the peptide is naturally found in Escherichia coli (bacteria).
References: UniProt: P08837, UniProt: P0A284*PLUS, protein-Npi-phosphohistidine-sugar phosphotransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY, TOCSY, DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear NMR techniques.

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Sample preparation

DetailsContents: natural abundance synthetic peptide 5 mM peptide and 50 mM dihexanoyl phosphatidylglycerol
Solvent system: 90% H2O and 10% D2O
Sample conditionsIonic strength: no buffer / pH: 5.4 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe/nmrDraw2.1Delaglio, F.data processing
PIPP1Garrett, D.noe picking
XPLOR-NIH1.06Schwieters, C.D., Kuszewski, J., Tjandra, N, Clore, G.M.structural calculations
MOLMOL2K.1Koradi, R.structural analysis and viewing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 146 distances derived from the NOESY spectra. No dihedral angles or hydrogen-bond restraints were applied.
NMR representativeSelection criteria: most resemble the average structure.
NMR ensembleConformer selection criteria: No NOE violations greater than 0.20 A; rms difference for bond deviations from ideality less than 0.01 A; rms difference for angle deviations from ideality less than 2 ...Conformer selection criteria: No NOE violations greater than 0.20 A; rms difference for bond deviations from ideality less than 0.01 A; rms difference for angle deviations from ideality less than 2 degrees; Structures with the lowerest energies in the ensemble; Structures most resemble the average structure.
Conformers calculated total number: 100 / Conformers submitted total number: 20

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