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- PDB-1r4t: Solution structure of exoenzyme S -

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Basic information

Entry
Database: PDB / ID: 1r4t
TitleSolution structure of exoenzyme S
Componentsexoenzyme S
KeywordsTOXIN / EXOS / PSEUDOMONAS AERUGINOSA / GAP / VIRULENCE FACTOR / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


glycosyltransferase activity / nucleotidyltransferase activity / GTPase activator activity / toxin activity / extracellular region
Similarity search - Function
Virulence factor YopE uncharacterised domain / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / : / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Virulence factor YopE uncharacterised domain / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / : / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLangdon, G.M. / Leitner, D. / Labudde, D. / Kuhne, R. / Schmieder, P. / Aktories, K. / Oschkinat, H.O. / Schmidt, G.
CitationJournal: To be Published
Title: Solution structure of the N-terminal GTPase activating domain of Pseudomonas aeruginosa exoenzyme S
Authors: Langdon, G.M. / Leitner, D. / Labudde, D. / Kuhne, R. / Schmieder, P. / Aktories, K. / Oschkinat, H.O. / Schmidt, G.
History
DepositionOct 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: 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_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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: exoenzyme S


Theoretical massNumber of molelcules
Total (without water)16,2191
Polymers16,2191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 71structures with acceptable covalent geometry,structures with favorable non-bond energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: Protein exoenzyme S


Mass: 16219.230 Da / Num. of mol.: 1 / Fragment: GAP-DOMAIN (RESIDUES 96-234)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q93SQ1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D NOESY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
1512D TOCSY
1613D 15N-separated NOESY
NMR detailsText: This structure was determined using standard 3D homonuclear techniques.

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Sample preparation

DetailsContents: 0.5-1.2 mM exos [U-95% 13C; U-90% 15N]50mM phosphate buffer
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.05 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Sparky3.106Goddard and Knellerdata analysis
XwinNMR2.6Brukerprocessing
DYANA1.6Guentertstructure solution
Amber7Caserefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy
Conformers calculated total number: 71 / Conformers submitted total number: 23

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