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- PDB-2ml9: Solution structure of YSCUCN in a micellar complex with SDS -

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Basic information

Entry
Database: PDB / ID: 2ml9
TitleSolution structure of YSCUCN in a micellar complex with SDS
ComponentsYop proteins translocation protein U
KeywordsMEMBRANE PROTEIN / YERSINIA / TYPE III SECRETION SYSTEM / YSCU / SECRETION SPECIFICITY / SODIUM DODECYL SULFATE
Function / homologyType III exporter system, secretion apparatus protein BsaZ / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / protein secretion / plasma membrane / Yop proteins translocation protein U
Function and homology information
Biological speciesYersinia pseudotuberculosis IP 32953 (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsWeise, C.F. / Wolf-Watz, M.
CitationJournal: Biophys.J. / Year: 2014
Title: Negatively charged lipid membranes promote a disorder-order transition in the Yersinia YscU protein.
Authors: Weise, C.F. / Login, F.H. / Ho, O. / Grobner, G. / Wolf-Watz, H. / Wolf-Watz, M.
History
DepositionFeb 20, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Yop proteins translocation protein U


Theoretical massNumber of molelcules
Total (without water)6,8331
Polymers6,8331
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 least restraint violations, followed by selection by lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Yop proteins translocation protein U


Mass: 6832.867 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 211-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis IP 32953 (bacteria)
Gene: pYV0074, yscU / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P69987

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1413D HNCA
1513D HN(CO)CA
1613D HNHA

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Sample preparation

DetailsContents: 100 uM [U-99% 13C; U-99% 15N] protein-1, 30 mM sodium phosphate-2, 50 mM sodium chloride-3, 26 mM SDS-4, 92% H2O/8% D2O
Solvent system: 92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 uMprotein-1[U-99% 13C; U-99% 15N]1
30 mMsodium phosphate-21
50 mMsodium chloride-31
26 mMSDS-41
Sample conditionsIonic strength: 0.12 / pH: 6 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ANSIGKraulischemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
ProcheckNMRLaskowski and MacArthurrefinement
X-PLOR NIHrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: SIMULATED ANNEALING FROM EXTENDED STRUCTURE, MINIMIZATION IN TORSION ANGLE/CARTESIAN SPACE
NMR constraintsNOE constraints total: 203 / NOE intraresidue total count: 39 / NOE long range total count: 0 / NOE medium range total count: 45 / NOE sequential total count: 119 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 80 / Protein psi angle constraints total count: 80
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with least restraint violations, followed by selection by lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum distance constraint violation: 0.554 Å / Maximum lower distance constraint violation: 0.073 Å / Maximum torsion angle constraint violation: 2.29 ° / Maximum upper distance constraint violation: 0 Å / Representative conformer: 1
NMR ensemble rmsDihedral angles rms dev error: 0.53 ° / Distance rms dev: 0 Å / Distance rms dev error: 0 Å

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