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- PDB-2kyr: Solution structure of Enzyme IIB subunit of PTS system from Esche... -

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Basic information

Entry
Database: PDB / ID: 2kyr
TitleSolution structure of Enzyme IIB subunit of PTS system from Escherichia coli K12. Northeast Structural Genomics Consortium target ER315/Ontario Center for Structural Proteomics target ec0544
ComponentsFructose-like phosphotransferase enzyme IIB component 1
KeywordsTRANSFERASE / Fructose-like phosphotransferase enzyme IIB component 1 / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


protein-phosphocysteine-D-fructose-phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-fructose phosphotransferase / protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity / protein-phosphocysteine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / plasma membrane / cytoplasm
Similarity search - Function
Phosphotransferase system, fructose-specific IIB subunit / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 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
PTS system fructose-like EIIB component 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Yee, A. / Gutmanas, A. / Semest, A. / Montelione, G.T. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: To be Published
Title: Solution structure of Enzyme IIB subunit of PTS system from Escherichia coli K12, Northeast Structural Genomics Consortium target ER315/Ontario Center for Structural Proteomics target ec0544
Authors: Wu, B. / Yee, A. / Gutmanas, A. / Semest, A. / Arrowsmith, C.H.
History
DepositionJun 7, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _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: Fructose-like phosphotransferase enzyme IIB component 1


Theoretical massNumber of molelcules
Total (without water)12,0691
Polymers12,0691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fructose-like phosphotransferase enzyme IIB component 1 / PTS system fructose-like EIIB component 1


Mass: 12068.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fryB, ypdH, b2387, JW5389 / Production host: Escherichia coli (E. coli)
References: UniProt: P69808, 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 HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D (H)CCH-TOCSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-13C NOESY aromatic
11022D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] ec0544-1, 10 mM [U-100% 2H] TRIS-2, 300 mM sodium chloride-3, 10 uM zinc sulphate-4, 10 mM [U-100% 2H] DTT-5, 10 mM benzamidine-6, 1 % inhibitor cocktail-7, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-7% 13C; U-100% 15N] ec0544-8, 10 mM [U-100% 2H] TRIS-9, 300 mM sodium chloride-10, 10 uM zinc sulphate-11, 10 mM [U-100% 2H] DTT-12, 10 mM benzamidine-13, 1 % inhibitor cocktail-14, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMec0544-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-2[U-100% 2H]1
300 mMsodium chloride-31
10 uMzinc sulphate-41
10 mMDTT-5[U-100% 2H]1
10 mMbenzamidine-61
1 %inhibitor cocktail-71
0.5 mMec0544-8[U-7% 13C; U-100% 15N]2
10 mMTRIS-9[U-100% 2H]2
300 mMsodium chloride-102
10 uMzinc sulphate-112
10 mMDTT-12[U-100% 2H]2
10 mMbenzamidine-132
1 %inhibitor cocktail-142
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas, Arrowsmithprocessing
Sparky3.95Goddarddata analysis
Sparky3.95Goddardpeak picking
FAWN1Lemak, Arrowsmithchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
PSVSBhattacharya and Montelionenmr structure quality assessment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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