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- PDB-1txe: Solution structure of the active-centre mutant Ile14Ala of the hi... -

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Basic information

Entry
Database: PDB / ID: 1txe
TitleSolution structure of the active-centre mutant Ile14Ala of the histidine-containing phosphocarrier protein (HPr) from Staphylococcus carnosus
ComponentsPhosphocarrier protein HPr
KeywordsTRANSPORT PROTEIN / open-faced beta-sandwich / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


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 / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; / PTS HPR domain serine phosphorylation site signature. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesStaphylococcus carnosus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMoeglich, A. / Koch, B. / Hengstenberg, W. / Brunner, E. / Kalbitzer, H.R. / Structural Proteomics in Europe (SPINE)
Citation
Journal: Eur.J.Biochem. / Year: 2004
Title: Solution structure of the active-centre mutant I14A of the histidine-containing phosphocarrier protein from Staphylococcus carnosus
Authors: Moeglich, A. / Koch, B. / Gronwald, W. / Hengstenberg, W. / Brunner, E. / Kalbitzer, H.R.
#1: Journal: Protein Sci. / Year: 2000
Title: 15N and 1H NMR study of histidine containing protein (HPr) from Staphylococcus carnosus at high pressure
Authors: Kalbitzer, H.R. / Goerler, A. / Li, H. / Dubovskii, P.V. / Hengstenberg, W. / Kowolik, C. / Yamada, H. / Akasaka, K.
#2: Journal: APPL.MAGN.RESON. / Year: 1999
Title: Solution Structure of the Histidine-Containing Phosphocarrier Protein from Staphylococcus carnosus
Authors: Goerler, A. / Hengstenberg, W. / Kravanja, M. / Beneicke, W. / Maurer, T. / Kalbitzer, H.R.
#3: Journal: J.Am.Chem.Soc. / Year: 2003
Title: NMR-spectroscopic mapping of an engineered cavity in the I14A mutant of HPr from Staphylococcus carnosus using xenon
Authors: Groeger, C. / Moeglich, A. / Pons, M. / Koch, B. / Hengstenberg, W. / Kalbitzer, H.R. / Brunner, E.
#4: Journal: Proteins / Year: 2004
Title: DRESS: a database of REfined solution NMR structures
Authors: Nabuurs, S.B. / Nederveen, A.J. / Vranken, W. / Doreleijers, J.F. / Bonvin, A.M.J.J. / Vuister, G.W. / Vriend, G. / Spronk, C.A.E.M.
#5: Journal: Proteins / Year: 2003
Title: Refinement of protein structures in explicit solvent
Authors: Linge, J.P. / Williams, M.A. / Spronk, C.A.E.M. / Bonvin, A.M.J.J. / Nilges, M.
History
DepositionJul 4, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: 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: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)9,4771
Polymers9,4771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9476.568 Da / Num. of mol.: 1 / Mutation: I14A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus carnosus (bacteria) / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23534

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1333D 13C-separated NOESY
144HSQC
NMR detailsText: Residual dipolar couplings for the amide bond (HN-N) as well as between the atoms HA and HN have also been used as restraints for structure determination.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4mM HPrI14A, 20mM potassium phosphate pH 7.14, 100mM KCl5% D2O, 95% H2O
21.7mM HPrI14A U-15N, 20mM potassium phosphate pH 7.14, 100mM KCl5% D2O, 95% H2O
31.5mM HPrI14A U-15N,13C, 20mM potassium phosphate pH 7.14, 100mM KCl5% D2O, 95% H2O
40.9mM HPrI14A U-15N, 20mM potassium phosphate pH 7.14, 100mM KCl, 7.5% DIODPC/CHAPSO (4.3:1)5% D2O, 95% H2O
Sample conditionsIonic strength: 0.12 / pH: 7.14 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX8003

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Processing

NMR software
NameVersionDeveloperClassification
AUREMOL1Gronwald, Neidig, Kalbitzerdata analysis
XwinNMR2.6Brukercollection
CNS1Brungerstructure solution
CNS1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: TOTAL NUMBER OF NOES USED FOR THE CALCULATION: 1268, NUMBER OF INTRA-RESIDUE NOES USED FOR THE CALCULATION: 637, NUMBER OF SHORT RANGE NOES (I,J, I < J < I+5) USED FOR THE CALCULATION: 365, ...Details: TOTAL NUMBER OF NOES USED FOR THE CALCULATION: 1268, NUMBER OF INTRA-RESIDUE NOES USED FOR THE CALCULATION: 637, NUMBER OF SHORT RANGE NOES (I,J, I < J < I+5) USED FOR THE CALCULATION: 365, NUMBER OF LONG RANGE (I,J, J > I+4) NOES USED FOR THE CALCULATION: 266, NUMBER OF DIHEDRAL ANGLES RESTRAINTS USED FOR THE CALCULATION: 44, NUMBER OF HYDROGEN BOND RESTRAINTS USED FOR THE CALCULATION: 20, NUMBER OF 1HN/15NH RESIDUAL DIPOLAR COUPLINGS USED FOR THE CALCULATION: 49, NUMBER OF 1HN/1HA RESIDUAL DIPOLAR COUPLINGS USED FOR THE CALCULATION: 25
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 10

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