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- PDB-2wwv: NMR structure of the IIAchitobiose-IIBchitobiose complex of the N... -

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Basic information

Entry
Database: PDB / ID: 2wwv
TitleNMR structure of the IIAchitobiose-IIBchitobiose complex of the N,N'- diacetylchitoboise brance of the E. coli phosphotransferase system.
Components
  • N\,N'-DIACETYLCHITOBIOSE-SPECIFIC PHOSPHOTRANSFERASE ENZYME IIA COMPONENT
  • N\,N'-DIACETYLCHITOBIOSE-SPECIFIC PHOSPHOTRANSFERASE ENZYME IIB COMPONENT
KeywordsTRANSFERASE / KINASE / PHOSPHOTRANSFERASE SYSTEM / CHITOBIOSE / SUGAR TRANSPORT
Function / homology
Function and homology information


protein-Npi-phosphohistidine-N,N'-diacetylchitobiose phosphotransferase / protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / protein-containing complex / cytosol
Similarity search - Function
Phosphotransferase system, EIIB component, type 3 / PTS_EIIB type-3 domain profile. / 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, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit ...Phosphotransferase system, EIIB component, type 3 / PTS_EIIB type-3 domain profile. / 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, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Response regulator / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PTS system N,N'-diacetylchitobiose-specific EIIA component / PTS system N,N'-diacetylchitobiose-specific EIIB component
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
ESCHERICHIA COLI K-12 (bacteria)
MethodSOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE SIMULATED ANNEALING
Model type detailsMINIMIZED AVERAGE, MODEL 1
AuthorsSang, Y.S. / Cai, M. / Clore, G.M.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Solution Structure of the Iiachitobose-Iibchitobiose Complex of the N,N'-Diacetylchitobiose Branch of the Escherichia Coli Phosphotransfer System
Authors: Jung, Y.S. / Cai, M. / Clore, G.M.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: Solution Structure of Enzyme Iia(Chitobiose) from the N,N'-Diacetylchitobiose Branch of the Escherichia Coli Phosphotransferase System.
Authors: Tang, C. / Williams, D.C.J. / Ghirlando, R. / Clore, G.M.
#2: Journal: Structure / Year: 1997
Title: The Structure of an Energy-Coupling Protein from Bacteria, Iibcellobiose, Reveals Similarity to Eukaryotic Protein Tyrosine Phosphatases.
Authors: Van Montfort, R.L. / Pijning, T. / Kalk, K.H. / Reizer, J. / Saier, M.H.J. / Thunnissen, M.M. / Robillard, G.T. / Dijkstra, B.W.
#3: Journal: J.Mol.Biol. / Year: 2001
Title: NMR Structure of Cysteinyl-Phosphorylated Enzyme Iib of the N,N'-Diacetylchitobiose-Specific Phosphoenolpyruvate-Dependent Phosphotransferase System of Escherichia Coli.
Authors: Ab, E. / Schuurman-Wolters, G.K. / Nijlant, D. / Dijkstra, K. / Saier, M.H. / Robillard, G.T. / Scheek, R.M.
History
DepositionOct 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references / Other ...Database references / Other / Source and taxonomy / Version format compliance
Revision 1.2Apr 19, 2017Group: Other
Revision 1.3Oct 16, 2019Group: Data collection / Other ...Data collection / Other / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_software
Item: _entity.src_method / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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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: N\,N'-DIACETYLCHITOBIOSE-SPECIFIC PHOSPHOTRANSFERASE ENZYME IIB COMPONENT


Theoretical massNumber of molelcules
Total (without water)44,7904
Polymers44,7904
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-49 kcal/mol
Surface area20870 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)91 / 91RESTRAINED REGULARIZED MEAN
RepresentativeModel #1

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Components

#1: Protein N\,N'-DIACETYLCHITOBIOSE-SPECIFIC PHOSPHOTRANSFERASE ENZYME IIA COMPONENT / IIACHB / PTS SYSTEM N\ / N'-DIACETYLCHITOBIOSE-SPECIFIC EIIA COMPONENT / EIIA-CHB / EIII-CHB


Mass: 11247.152 Da / Num. of mol.: 3 / Fragment: RESIDUES 14-116 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: P69791, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein N\,N'-DIACETYLCHITOBIOSE-SPECIFIC PHOSPHOTRANSFERASE ENZYME IIB COMPONENT / IIBCHB / PTS SYSTEM N\ / N'-DIACETYLCHITOBIOSE-SPECIFIC EIIB COMPONENT


Mass: 11049.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: P69795, protein-Npi-phosphohistidine-sugar phosphotransferase
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 89 TO GLU ENGINEERED RESIDUE IN CHAIN A, ASP 92 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, HIS 89 TO GLU ENGINEERED RESIDUE IN CHAIN A, ASP 92 TO LEU ENGINEERED RESIDUE IN CHAIN B, HIS 89 TO GLU ENGINEERED RESIDUE IN CHAIN B, ASP 92 TO LEU ENGINEERED RESIDUE IN CHAIN C, HIS 89 TO GLU ENGINEERED RESIDUE IN CHAIN C, ASP 92 TO LEU
Sequence detailsRESIDUE 1 IN CHAINS A, B AND C CORRESPONDS TO RESIDUE 14 OF WILD TYPE IIACHB, RESIDUE 76 IS A HIS ...RESIDUE 1 IN CHAINS A, B AND C CORRESPONDS TO RESIDUE 14 OF WILD TYPE IIACHB, RESIDUE 76 IS A HIS CHAIN D WAS PROVIDED WITH UNIPROT SEQUENCE REFERENCE P69795 BUT IS SYNTHETICALLY SYNTHESIZED.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOE
121ISOTOPE FILTERED/EDITED NOE
131RDC
141TRIPLE RESONANCE CORRELATION
NMR detailsText: NONE

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 308.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX6003
Bruker DRXBrukerDRX8004
Bruker DRXBrukerDRX9005

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.23SCHWIETERS, KUSZEWSKI,CLORErefinement
Xplor-NIHstructure solution
RefinementMethod: CONJOINED RIGID BODY, TORSION ANGLE SIMULATED ANNEALING
Software ordinal: 1
Details: THE STRUCTURE OF THE COMPLEX WAS SOLVED BY CONJOINED RIGID BODY/TORSION ANGLE SIMULATED ANNEALING USING XPLOR-NIH. THE CALCULATIONS ARE BASED ON 40 INTERMOLECULAR INTERPROTON DISTANCE ...Details: THE STRUCTURE OF THE COMPLEX WAS SOLVED BY CONJOINED RIGID BODY/TORSION ANGLE SIMULATED ANNEALING USING XPLOR-NIH. THE CALCULATIONS ARE BASED ON 40 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS, 78 INTRAMOLECULAR INTERPROTON DISTANCE RESTRAINTS RELATED ONLY TO THE ACTIVE SITE LOOP OF IIBCHB, 82 TORSION ANGLE RESTRAINTS RELATED TO THE BACKBONE OF THE ACTIVE SITE LOOP OF IIBCHB (RESIDUES 9-16, CHAIN D) AND THE INTERFACIAL SIDE CHAINS, 153 DIPOLAR COUPLINGS RELATED TO IIBCHB, AND 15 13CALPHA/13CBETA CHEMICAL SHIFT RESTRAINTS RELATED TO THE ACTIVE SITE LOOP OF IIBCHB. WITH THE EXCEPTION OF THE ACTIVE SITE LOOP OF IIBCHB (RESIDUES 9-16 OF CHAIN D) AND A MOBILE LOOP OF IIACHB (RESIDUES 62-71 OF CHAINS A, B, C) THE BACKBONE OF THE TWO PROTEINS AND NON-INTERFACIAL SIDE CHAINS ARE TREATED AS RIGID BODIES WITH ROTATIONAL AND TRANSLATIONAL DEGREES OF FREEDOM. THE COORDINATES FOR THE PORTIONS TREATED AS RIGID BODIES ARE TAKEN FROM THE X-RAY STRUCTURE OF IIBCHB (PDB CODE 1IIB) AND THE NMR STRUCTURE OF IIACHB (PDB CODE 1WCR). THE BACKBONE OF RESIDUES 9-16 OF CHAIN D, 62-71 OF CHAINS A, B AND C, AND THE INTERFACIAL SIDE CHAINS ARE GIVEN FULL TORSIONAL DEGREES OF FREEDOM. THE TARGET FUNCTION COMPRISES NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, RDC RESTRAINTS, 13CALPHA/13CBETA CHEMICAL SHIFT RESTRAINTS, A QUARTIC VAN DER WAALS REPULSION TERM FOR THE NON-BONDED CONTACTS, A MULTIDIMENSIONAL TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE, AND A GYRATION VOLUME POTENTIAL TO ENSURE OPTIMAL PACKING. FURTHER DETAILS ARE GIVEN IN THE ASSOCIATED PUBLICATION.
NMR ensembleConformer selection criteria: RESTRAINED REGULARIZED MEAN / Conformers calculated total number: 91 / Conformers submitted total number: 91

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