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- PDB-5t17: NMR structure of the E. coli protein NPr, residues 1-85 -

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Basic information

Entry
Database: PDB / ID: 5t17
TitleNMR structure of the E. coli protein NPr, residues 1-85
ComponentsPhosphocarrier protein NPr
KeywordsTRANSFERASE / PTSNtr / phosphotransfer protein / HPr-like / biofilm
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / phosphoenolpyruvate-dependent sugar phosphotransferase system / : / cytoplasm
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein NPr / Phosphocarrier protein NPr
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, G. / Li, X. / Peterkofsky, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Amino Acids / Year: 2008
Title: Solution structure of NPr, a bacterial signal-transducing protein that controls the phosphorylation state of the potassium transporter-regulating protein IIA Ntr.
Authors: Li, X. / Peterkofsky, A. / Wang, G.
History
DepositionAug 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphocarrier protein NPr


Theoretical massNumber of molelcules
Total (without water)9,2551
Polymers9,2551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Phosphocarrier protein NPr / Nitrogen-related HPr


Mass: 9254.570 Da / Num. of mol.: 1 / Fragment: UNP residues 1-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ptsO, Z4569, ECs4085 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: P0A9N2, UniProt: P0A9N0*PLUS, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY
131isotropic14D HNHC NOESY
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D HNCA
171isotropic13D C(CO)NH
181isotropic13D H(CCO)NH
191isotropic13D HNHA
1101isotropic13D HBHA(CO)NH
1111isotropic13D (H)CCH-TOCSY
1121isotropic13D (H)CCH-COSY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O
Label: NPr / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNPr[U-13C; U-15N]1
25 mMTrisnatural abundance1
Sample conditionsIonic strength: 25 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 308 K

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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
NameDeveloperClassification
PIPPGarrettchemical shift assignment
PIPPGarrettpeak picking
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 30

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