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- PDB-5gqs: NMR based solution structure of PTS system, galactitol-specific I... -

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Basic information

Entry
Database: PDB / ID: 5gqs
TitleNMR based solution structure of PTS system, galactitol-specific IIB component from methicillin resistant Staphylococcus aureus
ComponentsPTS galactitol transporter subunit IIB
KeywordsTRANSPORT PROTEIN / A four stranded parallel beta sheet / two alpha helices
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system
Similarity search - Function
Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS galactitol transporter subunit IIB / PTS system component, putative
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR
AuthorsWahab, A. / Schwalbe, H. / Shahid, M.F. / Richter, C. / Jonker, H.R.A.
CitationJournal: To Be Published
Title: NMR based solution structure of PTS system, galactitol-specific IIB component from methicillin resistant Staphylococcus aureus
Authors: Wahab, A. / Schwalbe, H. / Shahid, M.F. / Richter, C. / Jonker, H.R.A.
History
DepositionAug 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_prerelease_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _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: PTS galactitol transporter subunit IIB


Theoretical massNumber of molelcules
Total (without water)10,1911
Polymers10,1911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein PTS galactitol transporter subunit IIB


Mass: 10190.821 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Cell: Bacterium / Gene: QU38_14570 / Cell (production host): T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D1JRP2, UniProt: Q2G2B6*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D HN(CA)CB
131isotropic23D HNCO
141isotropic23D 1H-15N NOESY
151isotropic13D 1H-13C NOESY aliphatic
161isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 11.79 mg/mL 15N, 13C PTS system, galactitol-specific IIB component, 95% H2O/5% D2O
Details: Double labeled PTS protein / Label: 15N, 13C labeled / Solvent system: 95% H2O/5% D2O
SampleConc.: 11.79 mg/mL / Component: PTS system, galactitol-specific IIB component / Isotopic labeling: 15N, 13C
Sample conditionsDetails: 1.1 mM [U-13C6, 99%; 15N, 99%] protein, 50 mM Sodium Phosphate buffer, 50 mM NaCl, 1 mM DTT, 0.03% NaN3, 95% H2O/5% D2O, pH 6.9
Ionic strength: 50 mM Sodium Phosphate, 50 mM NaCl mM / Ionic strength err: 0 / Label: 15N, 13C / pH: 6.9 / PH err: 0 / Pressure: ambient / Pressure err: 0 / Temperature: 298 K / Temperature err: 0

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.114T. D. Goddard and D. G. Knellerchemical shift assignment
Sparky3.114T. D. Goddard and D. G. Knellerpeak picking
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
Sparky3.114T. D. Goddard and D. G. Knellerdata analysis
TopSpin3.5Bruker Biospinprocessing
TopSpin3.2Bruker Biospincollection
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.8.4.2Keller and Wuthrichdata analysis
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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