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- PDB-1rrz: Solution structure of GlgS protein from E. coli -

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Basic information

Entry
Database: PDB / ID: 1rrz
TitleSolution structure of GlgS protein from E. coli
ComponentsGlycogen synthesis protein glgSGlycogenesis
KeywordsSTRUCTURAL GENOMICS / BIOSYNTHETIC PROTEIN / all-helical domain / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


: / negative regulation of single-species biofilm formation on inanimate substrate / negative regulation of bacterial-type flagellum-dependent cell motility
Similarity search - Function
Glycogen synthesis protein GlgS / Surface composition regulator / GlgS superfamily / Glycogen synthesis protein / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Surface composition regulator
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsKozlov, G. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: BMC Biol. / Year: 2004
Title: Structure of GlgS from Escherichia coli suggests a role in protein-protein interactions.
Authors: Kozlov, G. / Elias, D. / Cygler, M. / Gehring, K.
History
DepositionDec 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen synthesis protein glgS


Theoretical massNumber of molelcules
Total (without water)10,0731
Polymers10,0731
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)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Glycogen synthesis protein glgS / Glycogenesis


Mass: 10073.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GLGS, B3049 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26649

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1222D NOESY
1332D NOESY
NMR detailsText: This structure was determined using standard triple-resonance and homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM GlgS U-15N; 5mM potassium phosphate; 1mM DTT; 0.1mM sodium azide90% H2O/10% D2O
21mM GlgS; 5mM potassium phosphate; 1mM DTT; 0.1mM sodium azide90% H2O/10% D2O
31mM GlgS; 5mM potassium phosphate; 1mM DTT; 0.1mM sodium azide100% D2O
Sample conditionsIonic strength: 5mM potassium phosphate / pH: 6.7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Bruker Biospincollection
XwinNMR2.1Bruker Biospinprocessing
XEASY1.3.13Wuthrichdata analysis
CYANA1.0.6Guentertstructure solution
Xplor-NIH2.9.2Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 449 restraints, 311 are NOE-derived distance constraints, 109 TALOS-derived dihedral angle restraints, 29 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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