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- PDB-2jzh: structure of IIB domain of the mannose transporter of E. coli -

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Basic information

Entry
Database: PDB / ID: 2jzh
Titlestructure of IIB domain of the mannose transporter of E. coli
ComponentsPTS system mannose-specific EIIAB component
KeywordsTRANSFERASE / Mannose specific PTS system IIAB / IIB domain / IIBMan phosphotransferase enzyme II / B component / Cytoplasm / Membrane / Phosphoprotein / Phosphotransferase system / Sugar transport / Transport
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 superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / 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 / simulated annealing in torsion angle space
Model type detailsminimized average
AuthorsKomlosh, M. / Williams Jr., D.C.
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 8, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS system mannose-specific EIIAB component


Theoretical massNumber of molelcules
Total (without water)19,1191
Polymers19,1191
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 / 130all calculated structures
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: 19119.258 Da / Num. of mol.: 1 / 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D (H)CCH-TOCSY
1213D (H)CCH-COSY
1313D 1H-13C NOESY
1422D 1H-15N HSQC
1523D 1H-15N NOESY
1623D CBCA(CO)NH
1723D C(CO)NH
1823D HN(CA)CB
1923D HBHA(CO)NH
11023D H(CCO)NH
NMR detailsText: Double and triple resonance 3D NMR experiments for assignments (HNCACB, CBCA(CO)NH, HBHA(CBCACO)NH, C(CCO)NH, H(CCO)NH, HCCH-COSY, HCCH-TOCSY). NOE-derived interproton distance restrants from ...Text: Double and triple resonance 3D NMR experiments for assignments (HNCACB, CBCA(CO)NH, HBHA(CBCACO)NH, C(CCO)NH, H(CCO)NH, HCCH-COSY, HCCH-TOCSY). NOE-derived interproton distance restrants from 3D 15N-, 13C-, 13C/15M-, 13C/13C, and 15N/15N-separated NOE spectra. Side chain rotamers from 3H heteronuclear couplings and short mixing time 3D 13C-separated NOE and 3D 15N-seaparated ROE spectra. RDCs obtained by taking difference in J couplings in aligned (phage pf1 and PEG/hexanol) and isotopic media.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 13C; U-100% 15N] protein, sodium phosphate, sodium azide, 100% D2O100% D2O
20.5-1 mM [U-100% 15N] protein, sodium phosphate, sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMsodium phosphate, sodium azide[U-100% 13C; U-100% 15N]1
0.5 mMsodium phosphate, sodium azide[U-100% 15N]2
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
PIPPGarrett and Clorechemical shift assignment
PIPPGarrett and Cloredata analysis
X-PLOR NIH2.18.1Schwieters, Kuszewski and Clorerefinement
CAPPGarrett and Clorechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing in torsion angle space / Software ordinal: 1
Details: RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS (NUNMER OF RESTRAINTS IN PARENTHESES): INTERPROTON DISTANCES (A) (1577) 0.008, TORSION ANGLES (DEG) (478) 0.26, 13CALPHA SHIFTS (PPM) (161) 1.25, ...Details: RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS (NUNMER OF RESTRAINTS IN PARENTHESES): INTERPROTON DISTANCES (A) (1577) 0.008, TORSION ANGLES (DEG) (478) 0.26, 13CALPHA SHIFTS (PPM) (161) 1.25, 13CBETA SHIFTS (PPM) (158) 1.23. RDC R-factors (%): PHAGE 1DNH (151) 4.2, PHAGE 1DNC' (113) 18.2, PHAGE 2DHNC' (113) 16.5, PEG/HEXANOL 1DNH (141) 6.0, PEG/HEXANOL 1DNC' (96) 25.8, PEG/HEXANOL 2DHNC' (103) 23.5.
NMR constraintsNOE constraints total: 1467 / NOE intraresidue total count: 451 / NOE long range total count: 339 / NOE medium range total count: 270 / NOE sequential total count: 407 / Protein chi angle constraints total count: 108 / Protein other angle constraints total count: 53 / Protein phi angle constraints total count: 160 / Protein psi angle constraints total count: 157
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures / Conformers calculated total number: 130 / Conformers submitted total number: 1
NMR ensemble rmsDistance rms dev: 0.006 Å / Distance rms dev error: 0.001 Å

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