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- PDB-5woy: NMR solution structure of Enzyme I (nEIt) protein using two 4D-spectra -

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Basic information

Entry
Database: PDB / ID: 5woy
TitleNMR solution structure of Enzyme I (nEIt) protein using two 4D-spectra
ComponentsPhosphoenolpyruvate-protein phosphotransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / metal ion binding / cytoplasm
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 / Glucose Oxidase; domain 1 / Pyruvate kinase-like domain superfamily / Enzyme I; Chain A, domain 2 / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Phosphoenolpyruvate-protein phosphotransferase
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodSOLUTION NMR / na
AuthorsEvangelidis, T. / Nerli, S. / Sgourakis, N.G. / Tripsianes, K.
CitationJournal: Nat Commun / Year: 2018
Title: Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra.
Authors: Evangelidis, T. / Nerli, S. / Novacek, J. / Brereton, A.E. / Karplus, P.A. / Dotas, R.R. / Venditti, V. / Sgourakis, N.G. / Tripsianes, K.
History
DepositionAug 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate-protein phosphotransferase


Theoretical massNumber of molelcules
Total (without water)27,2971
Polymers27,2971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13400 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 27297.273 Da / Num. of mol.: 1 / Fragment: PEP-utilizers residues 1-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: PtsA, TTE2334 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8R7R4, phosphoenolpyruvate-protein phosphotransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic14D HC(CC TOCSY(CO))NH
121isotropic14D 13C,15N edited HMQC-NOESY-HSQC
131isotropic14D 13C,13C edited HMQC-NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 1.8 mM [U-13C; U-15N] Enzyme I (nEIt) protein, 95% H2O/5% D2O
Label: 13C_15N_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.8 mM / Component: Enzyme I (nEIt) protein / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
4D-CHAINSEvangelidis and Tripsianeschemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CS-ROSETTAShen, Vernon, Baker and Baxdata analysis
SparkyGoddardpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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