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- PDB-1wcr: Trimeric Structure of the Enzyme IIA from Escherichia coli Phosph... -

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Basic information

Entry
Database: PDB / ID: 1wcr
TitleTrimeric Structure of the Enzyme IIA from Escherichia coli Phosphotransferase System Specific for N,N'-Diacetylchitobiose
ComponentsPTS SYSTEM, N, N'-DIACETYLCHITOBIOSE-SPECIFIC IIA COMPONENT
KeywordsTRANSFERASE / IIA / PTS / MUTAGENESIS / CHITOBIOSE / SUGAR TRANSPORT / PHOSPHOTRANSFERASE
Function / homology
Function and homology information


protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / 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, lactose/cellobiose-type IIA subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PTS system N,N'-diacetylchitobiose-specific EIIA component / PTS system N,N'-diacetylchitobiose-specific EIIA component
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / SIMULATED ANNEALING IN TORSION ANG SPACE
Model type detailsMINIMIZED AVERAGE
AuthorsTang, C. / Clore, G.M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Solution Structure of Enzyme Iiachitobiose from the N,N'-Diacetylchitobiose Branch of the Escherichia Coli Phosphotransferase System
Authors: Tang, C. / Williams, D.C. / Ghirlando, R. / Clore, G.M.
History
DepositionNov 19, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS SYSTEM, N, N'-DIACETYLCHITOBIOSE-SPECIFIC IIA COMPONENT
B: PTS SYSTEM, N, N'-DIACETYLCHITOBIOSE-SPECIFIC IIA COMPONENT
C: PTS SYSTEM, N, N'-DIACETYLCHITOBIOSE-SPECIFIC IIA COMPONENT


Theoretical massNumber of molelcules
Total (without water)33,7693
Polymers33,7693
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 / 100RESTRAINED REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: Protein PTS SYSTEM, N, N'-DIACETYLCHITOBIOSE-SPECIFIC IIA COMPONENT / EIIA-CHB / N / N'-DIACETYLCHITOBIOSE-PERMEASE IIA COMPONENT / PHOSPHOTRANSFERASE ENZYME II A ...EIIA-CHB / N / N'-DIACETYLCHITOBIOSE-PERMEASE IIA COMPONENT / PHOSPHOTRANSFERASE ENZYME II A COMPONENT / EIII-CHB


Mass: 11256.186 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) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P17335, UniProt: P69791*PLUS, protein-Npi-phosphohistidine-sugar phosphotransferase
Compound detailsENGINEERED RESIDUE ASP 92 LEU (RESIDUE 79 IN COORDINATES).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111(1) TROSY TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN
121(2) QUANTITATIVE J CORRELATION FOR SIDECHAIN COUPLING CONSTANTS
131(3) 3D
1414D HETERONUCLEAR SEPARATED NOE EXPTS
151(4) TROSY HNCO AND HN(CO)CA EXPERIMENTS FOR DIPOLAR COUPLINGS. DIPOLAR COUPLINGS WERE MEASURED IN PF1 PHAGE
NMR detailsText: EXPERIMENTAL RESTRAINTS: 1290 INTERPROTON DISTANCE RESTRAINTS: 246 SEQUENTIAL, 258 MEDIUM-RANGE, 90 LONG-RANGE INTRAMOLECULAR RESTRAINTS; 234 INTERMOLECULAR DISTANCE RESTRAINTS; 462 DISTANCE ...Text: EXPERIMENTAL RESTRAINTS: 1290 INTERPROTON DISTANCE RESTRAINTS: 246 SEQUENTIAL, 258 MEDIUM-RANGE, 90 LONG-RANGE INTRAMOLECULAR RESTRAINTS; 234 INTERMOLECULAR DISTANCE RESTRAINTS; 462 DISTANCE RESTRAINTS FOR BACKBONE H-BONDS FOR 231 H-BONDS (71 PER SUBUNIT) 729 TORSION ANGLE RESTRAINTS (255 PHI, 255 PSI, 219 CHI) 585 CALPHA/CBETA CHEMICAL SHIFT RESTRAINTS 759 RESIDUAL DIPOLAR COUPLING RESTRAINTS (252 N-H, 255 N-C', 249 C'-CA) DIPOLAR COUPLING R-FACTORS FOR THE RESTRAINED REGULARIZED MEAN STRUCTURE N-H 7.1% N-C' 15.2% C'-CA 17.7%

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Sample preparation

Sample conditionsIonic strength: 10MM SODIUM PHOSPHATE / pH: 6.5 / Pressure: 1.0 atm / Temperature: 303.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX6003
Bruker DMXBrukerDMX7504
Bruker DRXBrukerDRX8005

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH)(HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH)SCHWIETERS, KUSZEWSKI, TJrefinement
XPLOR-NIHstructure solution
RefinementMethod: SIMULATED ANNEALING IN TORSION ANG SPACE / Software ordinal: 1
Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, 13CALPHA/BETA CHEMICAL SHIFT RESTRAINTS, AND RESIDUAL DIPOLAR COUPLING ...Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, 13CALPHA/BETA CHEMICAL SHIFT RESTRAINTS, AND RESIDUAL DIPOLAR COUPLING RESTRAINTS (N-H, N-C' AND C'-CA). NON-BONDED INTERACTIONS ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, TORSION ANGLE AND HYDROGEN BONDING DATABASE POTENTIALS OF MEAN FORCE, AND A RADIUS OF GYRATION RESTRAINT. IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE ATOMIC RMS DIFFERENCE IN ANGSTROMS BETWEEN THE 80 INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATES RESIDUES 1-3, 61-69 AND 102-103 ARE DISORDERED IN SOLUTION.
NMR ensembleConformer selection criteria: RESTRAINED REGULARIZED MEAN STRUCTURE
Conformers calculated total number: 100 / Conformers submitted total number: 1

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