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- PDB-1vkr: STRUCTURE OF IIB DOMAIN OF THE MANNITOL-SPECIFIC PERMEASE ENZYME II -

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Basic information

Entry
Database: PDB / ID: 1vkr
TitleSTRUCTURE OF IIB DOMAIN OF THE MANNITOL-SPECIFIC PERMEASE ENZYME II
Componentsmannitol-specific PTS system enzyme IIABC components
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / SUGAR TRANSPORT
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannitol phosphotransferase / protein-N(PI)-phosphohistidine-mannitol phosphotransferase system transmembrane transporter activity / protein-phosphocysteine-mannitol phosphotransferase system transporter activity / mannitol transmembrane transport / protein-phosphocysteine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / phosphorylation / plasma membrane
Similarity search - Function
Phosphotransferase system, mannitol-specific enzyme IIC / Phosphotransferase system EIIB component, mannitol-specific / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / PTS EIIA domains phosphorylation site signature 2. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphotransferase system, EIIC / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 ...Phosphotransferase system, mannitol-specific enzyme IIC / Phosphotransferase system EIIB component, mannitol-specific / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / PTS EIIA domains phosphorylation site signature 2. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphotransferase system, EIIC / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / Phosphotransferase system, EIIC / PTS_EIIA type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Phosphotransferase/anion transporter / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system mannitol-specific EIICBA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsClore, G.M. / Legler, P.M. / Cai, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Three-dimensional Solution Structure of the Cytoplasmic B Domain of the Mannitol Transporter II-Mannitol of the Escherichia coli Phosphotransferase System.
Authors: Legler, P.M. / Cai, M. / Peterkofsky, A. / Clore, G.M.
History
DepositionJun 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mannitol-specific PTS system enzyme IIABC components


Theoretical massNumber of molelcules
Total (without water)13,4621
Polymers13,4621
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 / 80REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: Protein mannitol-specific PTS system enzyme IIABC components / IIBMTL PHOSPHOTRANSFERASE ENZYME II / B COMPONENT / EIIB-MTL


Mass: 13462.077 Da / Num. of mol.: 1 / Fragment: IIB DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00550

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN
121(2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
131(3) 3D, 4D HETERONUCLEAR SEPARATED NOE EXPTS
141(4) IPAP and COUPLED HSQC EXPERIMENTS FOR DIPOLAR COUPLINGS. DIPOLAR COUPLINGS WERE MEASURED IN PEG/HEXANOL

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Sample preparation

Sample conditionsIonic strength: 40 mM SODIUM PHOSPHATE / pH: 7.1 / Temperature: 308.00 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002
Bruker DRX600BrukerDRX6007503
Bruker DMC750BrukerDMC7508004
Bruker DRX800BrukerDRX8008005

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Processing

NMR softwareName: X-PLOR NIH / Version: (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) / Developer: SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, 3JHN-HALPHA COUPLING CONSTANT RESTRAINTS, 13CALPHA/BETA CHEMICAL SHIFT ...Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, 3JHN-HALPHA COUPLING CONSTANT RESTRAINTS, 13CALPHA/BETA CHEMICAL SHIFT RESTRAINTS, AND RESIDUAL DIPOLAR COUPLING RESTRAINTS (N-H, N-C' AND HN-C'); A QUARTIC VAN DER WAALS REPULSION TERM, TORSION ANGLE AND HYDROGEN BONDING DATABASE POTENTIALS OF MEAN FORCE, AND A RADIUS OF GYRATION RESTRAINTS. IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED BEST-FITTED TO RESIDUES 375-471. ONLY RESIDUES 375-471 ARE SHOWN SINCE RESIDUES 365-374 AND 472-489 AT THE N- AND C-TERMINI RESPECTIVELY, ARE DISORDERED IN SOLUTION. EXPERIMENTAL RESTRAINTS: 1444 INTERPROTON DISTANCE RESTRAINTS: (90 INTRARESIDUE; 419 SEQUENTIAL, 347 MEDIUM-RANGE, AND 517 LONG-RANGE INTERRESIDUE; 50 SEQUENTIAL/MEDIUM-RANGE AMBIGUOUS; 21 LONG-RANGE AMBIGUOUS 110 DISTANCE RESTRAINTS FOR 55 BACKBONE H-BONDS 214 TORSION ANGLE RESTRAINTS (90 PHI, 94 PSI, 68 CHI) 189 CALPHA/CBETA CHEMICAL SHIFT RESTRAINTS 70 3JHN-HA COUPLING CONSTANT RESTRAINTS 200 RESIDUAL DIPOLAR COUPLING RESTRAINTS (74 N-H, 62 N-C', 64 HN-C') DIPOLAR COUPLING R-FACTORS: N-H 2.8% N-C' 14.9% HN-C' 13.5%
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 80 / Conformers submitted total number: 1

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