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- PDB-2l2q: Solution Structure of cellobiose-specific phosphotransferase IIB ... -

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Basic information

Entry
Database: PDB / ID: 2l2q
TitleSolution Structure of cellobiose-specific phosphotransferase IIB component protein from Borrelia burgdorferi
ComponentsPTS system, cellobiose-specific IIB component (CelA)
KeywordsTRANSFERASE / cellobiose-specific phosphotransferase IIB component / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SGC / SSGCID
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity
Similarity search - Function
Phosphotransferase system, EIIB component, type 3 / PTS_EIIB type-3 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
Chitibiose transporter protein chbB
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsYang, F. / Barnwal, R.P. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Solution Structure of cellobiose-specific phosphotransferase IIB component protein from Borrelia burgdorferi
Authors: Yang, F. / Barnwal, R.P. / Varani, G.
History
DepositionAug 25, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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 system, cellobiose-specific IIB component (CelA)


Theoretical massNumber of molelcules
Total (without water)11,9811
Polymers11,9811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein PTS system, cellobiose-specific IIB component (CelA)


Mass: 11980.933 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: BB_B06 / Plasmid: Ava Vector / Production host: Escherichia coli (E. coli)
References: UniProt: O50982, 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
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1332D 1H-1H NOESY
1432D 1H-1H TOCSY
1523D CBCA(CO)NH
1623D HN(CA)CB
1723D HNCO
1813D HNHA
1923D (H)CCH-TOCSY
11013D 1H-15N NOESY
11123D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-95% 15N] protein, 20 mM potassium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM [U-95% 13C; U-95% 15N] protein, 20 mM potassium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
31.1 mM protein, 20 mM potassium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMprotein-1[U-95% 15N]1
20 mMpotassium phosphate-21
100 mMpotassium chloride-31
1 mMDTT-41
1.2 mMprotein-5[U-95% 13C; U-95% 15N]2
20 mMpotassium phosphate-62
100 mMpotassium chloride-72
1 mMDTT-82
1.1 mMprotein-93
20 mMpotassium phosphate-103
100 mMpotassium chloride-113
1 mMDTT-123
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
MOLMOLKoradi, Billeter and Wuthrichstructure display
TopSpinBruker Biospincollection
CcpNMRCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SANEDuggan, Legge, Dyson & Wrightdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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