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- PDB-2jzo: Solution NMR structure of the non-productive complex between IIAM... -

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Basic information

Entry
Database: PDB / ID: 2jzo
TitleSolution NMR structure of the non-productive complex between IIAMannose and IIBMannose of the mannose transporter of the E. coli phosphotransferase system
Components(PTS system mannose-specific EIIAB component) x 2
KeywordsTRANSFERASE / phosphotransferase / sugar transport / complex transferase-phosphocarrier / Cytoplasm / Membrane / Phosphoprotein / Phosphotransferase system
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / protein homodimerization activity / membrane ...protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / protein homodimerization activity / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphotransferase system, mannose family IIA component / Phosphotransferase system, sorbose subfamily IIB component, subgroup / Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component ...Phosphotransferase system, mannose family IIA component / Phosphotransferase system, sorbose subfamily IIB component, subgroup / Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system mannose-specific EIIAB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / conjoined rigid body, torsion angle simulated annealing
Model type detailsminimized average
AuthorsClore, G. / Hu, J. / Hu, K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Solution NMR Structures of Productive and Non-productive Complexes between the A and B Domains of the Cytoplasmic Subunit of the Mannose Transporter of the Escherichia coli Phosphotransferase System.
Authors: Hu, J. / Hu, K. / Williams, D.C. / Komlosh, M.E. / Cai, M. / Clore, G.M.
History
DepositionJan 10, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS system mannose-specific EIIAB component
B: PTS system mannose-specific EIIAB component
D: PTS system mannose-specific EIIAB component


Theoretical massNumber of molelcules
Total (without water)47,2293
Polymers47,2293
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 120restrained regularized mean
RepresentativeModel #1minimized average structure

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Components

#1: Protein PTS system mannose-specific EIIAB component / EIIAB-Man / Mannose-specific phosphotransferase enzyme IIB component / PTS system mannose-specific ...EIIAB-Man / Mannose-specific phosphotransferase enzyme IIB component / PTS system mannose-specific EIIB component


Mass: 14448.452 Da / Num. of mol.: 2 / Fragment: PTS EIIB type-4 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: manX, gptB, ptsL / Plasmid: pET32a modified / Production host: Escherichia coli (E. coli)
References: UniProt: P69797, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Protein PTS system mannose-specific EIIAB component / EIIAB-Man / Mannose-specific phosphotransferase enzyme IIA component / PTS system mannose-specific ...EIIAB-Man / Mannose-specific phosphotransferase enzyme IIA component / PTS system mannose-specific EIIA component / EIII-Man /


Mass: 18332.271 Da / Num. of mol.: 1 / Fragment: PTS EIIA type-4 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: manX, gptB, ptsL / Plasmid: pET32a modified / Production host: Escherichia coli (E. coli)
References: UniProt: P69797, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111triple resonance
12212C-filtered/13C-separated NOE
13112C-SEPARATED/12C-FILTERED NOE
14213C-SEPARATED/15N-EDITED NOE
NMR detailsText: Triple resonance experiments for assignment. Quantitative J correlation experiments for heteronuclear scalar couplings. 3D and 2D isotope filtered/isotope-separated NOE experiments for intermolecular NOEs.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM IIAMan+IIBMan, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM IIAMan+IIBMan, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMIIAMan+IIBMansee details1
0.5 mMIIAMan+IIBMansee details2
Sample conditionsIonic strength: 20 mM phosphate / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002
Bruker DRX600BrukerDRX6006003
Bruker DRX800BrukerDRX8008004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.18.1Schwieters, Kuszewski, and Clorestructure solution
X-PLOR NIH2.18.1Schwieters, Kuszewski, and Clorerefinement
RefinementMethod: conjoined rigid body, torsion angle simulated annealing
Software ordinal: 1
Details: Backbone coordinates of productive IIAMan-IIBMan complex (2JZN) are held fixed, coordinates of IIBMan (1JZH) representing the non-productive complex is free to rotate and translate; the ...Details: Backbone coordinates of productive IIAMan-IIBMan complex (2JZN) are held fixed, coordinates of IIBMan (1JZH) representing the non-productive complex is free to rotate and translate; the interfacial side chains are given torsional degrees of freedom; atomic overlap is allowed between the two molecules of IIBMan representing the productive and non-productive complexes since the two complexes do not co-exist; and the interproton distance restraints are treated as (sigmar-6)-1/6 sums since the NOEs arise from a mixture of productive and non-productive complexes. Further details in publication.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: restrained regularized mean / Conformers calculated total number: 120 / Conformers submitted total number: 1
NMR ensemble rmsDistance rms dev: 0.02 Å

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