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- PDB-2lrl: Solution Structures of the IIA(Chitobiose)-HPr complex of the N,N... -

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Basic information

Entry
Database: PDB / ID: 2lrl
TitleSolution Structures of the IIA(Chitobiose)-HPr complex of the N,N'-Diacetylchitobiose Branch of the Escherichia coli Phosphotransferase System
Components
  • N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component
  • Phosphocarrier protein HPr
KeywordsTRANSFERASE / protein-protein complex
Function / homology
Function and homology information


protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / transmembrane transporter complex / enzyme regulator activity ...protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / transmembrane transporter complex / enzyme regulator activity / enzyme activator activity / protein-containing complex / cytosol
Similarity search - Function
Phosphotransferase system, lactose/cellobiose-type IIA subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit superfamily / PTS system, Lactose/Cellobiose specific IIA subunit / PTS_EIIA type-3 domain profile. / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Phosphotransferase system, lactose/cellobiose-type IIA subunit ...Phosphotransferase system, lactose/cellobiose-type IIA subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit superfamily / PTS system, Lactose/Cellobiose specific IIA subunit / PTS_EIIA type-3 domain profile. / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHITE ION / Phosphocarrier protein HPr / PTS system N,N'-diacetylchitobiose-specific EIIA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 20
AuthorsJung, Y. / Cai, M. / Clore, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Solution Structure of the IIAChitobiose-HPr Complex of the N,N'-Diacetylchitobiose Branch of the Escherichia coli Phosphotransferase System.
Authors: Jung, Y.S. / Cai, M. / Clore, G.M.
History
DepositionApr 6, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component
B: N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component
C: N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component
D: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9775
Polymers42,8984
Non-polymers791
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein N,N'-diacetylchitobiose-specific phosphotransferase enzyme IIA component / EIIA-Chb / EIII-Chb / PTS system N / N'-diacetylchitobiose-specific EIIA component


Mass: 11256.186 Da / Num. of mol.: 3 / Fragment: PTS EIIA type-3 residues 14-116 / Mutation: D79L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: chbA, celC, b1736, JW1725 / Production host: Escherichia coli (E. coli)
References: UniProt: P69791, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9129.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ptsH, hpr, b2415, JW2408 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AA04, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases
#3: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(COCA)CB
1413D HNCA
151c13-c12 edited/filted NOESY

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Sample preparation

DetailsContents: 1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMH2O-1[U-99% 13C; U-99% 15N]1
1.0 mMD2O-21
Sample conditionsIonic strength: 0.02 / pH: 7.4 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloredata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorechemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: conjoined rigid body/torsion angle simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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