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- PDB-1ax3: SOLUTION NMR STRUCTURE OF B. SUBTILIS IIAGLC, 16 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1ax3
TitleSOLUTION NMR STRUCTURE OF B. SUBTILIS IIAGLC, 16 STRUCTURES
ComponentsGLUCOSE PERMEASE IIA DOMAIN
KeywordsPHOSPHOTRANSFERASE SYSTEM / SUGAR TRANSPORT / TRANSFERASE / PHOSPHORYLATION / TRANSMEMBRANE
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-glucose phosphotransferase / protein-phosphocysteine-sugar phosphotransferase activity / protein-N(pi)-phosphohistidine--N-acetyl-D-glucosamine phosphotransferase activity / glucose transmembrane transporter activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / phosphorylation / plasma membrane
Similarity search - Function
Phosphotransferase system, maltose/glucose-specific subfamily IIC component / PTS system glucose-specific IIBC component / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. ...Phosphotransferase system, maltose/glucose-specific subfamily IIC component / PTS system glucose-specific IIBC component / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
PTS system glucose-specific EIICBA component
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, MOLECULAR DYNAMICS
AuthorsChen, Y. / Case, D.A. / Reizer, J. / Saier Junior, M.H. / Wright, P.E.
CitationJournal: Proteins / Year: 1998
Title: High-resolution solution structure of Bacillus subtilis IIAglc.
Authors: Chen, Y. / Case, D.A. / Reizer, J. / Saier Jr., M.H. / Wright, P.E.
History
DepositionOct 25, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSE PERMEASE IIA DOMAIN


Theoretical massNumber of molelcules
Total (without water)17,3971
Polymers17,3971
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)16 / 100LEAST RESTRAINT VIOLATION AND LOWEST AMBER ENERGY
Representative

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Components

#1: Protein GLUCOSE PERMEASE IIA DOMAIN / IIAGLC


Mass: 17396.787 Da / Num. of mol.: 1 / Fragment: A DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PRE / Production host: Escherichia coli (E. coli) / Strain (production host): MZ1
References: UniProt: P20166, 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
111NOESY
121DQF-COSY
131TOCSY
141HMQC-J

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Sample preparation

Sample conditionspH: 6.87 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker AMX600BrukerAMX6006002

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
DISGEOstructure solution
Amberstructure solution
RefinementMethod: DISTANCE GEOMETRY, MOLECULAR DYNAMICS / Software ordinal: 1 / Details: REFINEMENT DETAILS CAN BE FOUND IN THE PAPER.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND LOWEST AMBER ENERGY
Conformers calculated total number: 100 / Conformers submitted total number: 16

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