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- PDB-2n5t: Ensemble solution structure of the phosphoenolpyruvate-Enzyme I c... -

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Basic information

Entry
Database: PDB / ID: 2n5t
TitleEnsemble solution structure of the phosphoenolpyruvate-Enzyme I complex from the bacterial phosphotransferase system
ComponentsPhosphoenolpyruvate-protein phosphotransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / N-acetylglucosamine transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / metal ion binding / identical protein binding / cytosol
Similarity search - Function
PtsI, HPr-binding domain / Phosphotransferase system, enzyme I / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / : / PEP-utilising enzyme, N-terminal / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. ...PtsI, HPr-binding domain / Phosphotransferase system, enzyme I / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / : / PEP-utilising enzyme, N-terminal / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Phosphoenolpyruvate-binding domains / Glucose Oxidase; domain 1 / Enzyme I; Chain A, domain 2 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / 3-Layer(bba) Sandwich / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Phosphoenolpyruvate-protein phosphotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
Model detailslowest energy, model1
AuthorsVenditti, V. / Schwieters, C.D. / Grishaev, A. / Clore, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering.
Authors: Venditti, V. / Schwieters, C.D. / Grishaev, A. / Clore, G.M.
History
DepositionJul 28, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Apr 17, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Refinement description / Structure summary
Category: pdbx_nmr_exptl_sample / pdbx_nmr_refine ...pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_software / struct
Item: _pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling ..._pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_software.name / _struct.title
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate-protein phosphotransferase
B: Phosphoenolpyruvate-protein phosphotransferase


Theoretical massNumber of molelcules
Total (without water)127,2712
Polymers127,2712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3478.4 Å2
ΔGint-21.1 kcal/mol
Surface area54430.8 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Phosphoenolpyruvate-protein phosphotransferase / Phosphotransferase system / enzyme I


Mass: 63635.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ptsI, b2416, JW2409 / Production host: Escherichia coli (E. coli)
References: UniProt: P08839, phosphoenolpyruvate-protein phosphotransferase

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Experimental details

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Experiment

Experiment
MethodDetails (eV)
SOLUTION NMREnsemble Solution structure of the phosphoenolpyruvate-Enzyme I complex from the bacterial hosphotransferase system as determined by NMR residual dipolar couplings and solution X-ray scattering
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111ARTSY
1212D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.4 mM [U-13C; U-15N; U-2H] EIA, 20 mM TRIS, 1 mM EDTA, 100 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMEIA[U-13C; U-15N; U-2H]1
20 mMTRISnatural abundance1
1 mMEDTAnatural abundance1
100 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
Sample conditionsIonic strength: 0.1 / pH: 7.4 / Pressure: ambient / Temperature: 310 K

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Data collection

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 2
Details: The deposited structures represent two-membered ensembles with varying weights which must be considered together to properly reproduce the RDC and SAXS data. The first members of 10 ...Details: The deposited structures represent two-membered ensembles with varying weights which must be considered together to properly reproduce the RDC and SAXS data. The first members of 10 ensembles are reported in models 1-10 which were allowed rigid-body motion of subunits, arbitrary motion of linker regions and torsion degrees of freedom for sidechains. The second member of each ensemble is represented in model 11, which was fixed in the calculations. The ten pairs of weights for the ten ensemble members are Ensemble 1: MODEL 1, weight: 0.503 MODEL 11, weight: 0.497 Ensemble 2: MODEL 2, weight: 0.518 MODEL 11, weight: 0.482 Ensemble 3: MODEL 3, weight: 0.526 MODEL 11, weight: 0.474 Ensemble 4: MODEL 4, weight: 0.520 MODEL 11, weight: 0.480 Ensemble 5: MODEL 5, weight: 0.508 MODEL 11, weight: 0.492 Ensemble 6: MODEL 6, weight: 0.531 MODEL 11, weight: 0.469 Ensemble 7: MODEL 7, weight: 0.498 MODEL 11, weight: 0.501 Ensemble 8: MODEL 8, weight: 0.524 MODEL 11, weight: 0.476 Ensemble 9: MODEL 9, weight: 0.514 MODEL 11, weight: 0.486 Ensemble 10: MODEL 10, weight: 0.526 MODEL 11, weight: 0.474
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 11 / Maximum torsion angle constraint violation: 19.4 °

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