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- PDB-1poq: Solution Structure of a Superantigen from Yersinia pseudotuberculosis -

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Basic information

Entry
Database: PDB / ID: 1poq
TitleSolution Structure of a Superantigen from Yersinia pseudotuberculosis
ComponentsYPM
KeywordsIMMUNE SYSTEM / Jelly roll fold
Function / homologyMitogen Ypm / Mitogen, Yersinia pseudotuberculosis / Mitogen Ypm superfamily / Yersinia pseudo-tuberculosis mitogen / Jelly Rolls / Sandwich / Mainly Beta / -derived mitogen
Function and homology information
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsDonadini, R. / Liew, C.W. / Kwan, A.H. / Mackay, J.P. / Fields, B.A.
CitationJournal: Structure / Year: 2004
Title: Crystal and Solution Structures of a Superantigen from Yersinia pseudotuberculosis Reveal a Jelly-Roll Fold.
Authors: Donadini, R. / Liew, C.W. / Kwan, A.H. / Mackay, J.P. / Fields, B.A.
History
DepositionJun 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YPM


Theoretical massNumber of molelcules
Total (without water)13,1111
Polymers13,1111
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein YPM


Mass: 13110.629 Da / Num. of mol.: 1 / Fragment: YPM(residues 33-151)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: ypmA / Plasmid: pMAL-p2x / Production host: Escherichia coli (E. coli) / Strain (production host): Novablue / References: UniProt: Q57221
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
141HNHA
151HN(CO)CA
161HNCA
171CBCA(CO)NH
181HN(CA)CB
NMR detailsText: This structure was determined using standard 2D homonuclear and triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.5mM YPM protein (33-151), 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6.5 / 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 DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
XEASY1.3.13Bartels et aldata analysis
DYANA1.5Guntert et alrefinement
ARIA1.1.2Linge et alstructure solution
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: Final structures were based on 1934 unambiguous NOE-derived distance constraints, 139 ambiguous constraints, 135 dihedral angle restraints and 26 hydrogen bond distance restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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