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- PDB-2kv7: NMR solution structure of a soluble PrgI mutant from Salmonella T... -

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Basic information

Entry
Database: PDB / ID: 2kv7
TitleNMR solution structure of a soluble PrgI mutant from Salmonella Typhimurium
ComponentsProtein prgI
KeywordsPROTEIN TRANSPORT / PrgI / bacterial pathogenesis / type three secretion needle / needle protomer / Transport / Virulence
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / identical protein binding
Similarity search - Function
Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein
Similarity search - Domain/homology
SPI-1 type 3 secretion system needle filament protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSchmidt, H. / Poyraz, O. / Seidel, K. / Delissen, F. / Ader, C. / Tenenboim, H. / Goosmann, C. / Laube, B. / Thuenemann, A.F. / Zychlinski, A. ...Schmidt, H. / Poyraz, O. / Seidel, K. / Delissen, F. / Ader, C. / Tenenboim, H. / Goosmann, C. / Laube, B. / Thuenemann, A.F. / Zychlinski, A. / Baldus, M. / Lange, A. / Griesinger, C. / Kolbe, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Protein refolding is required for assembly of the type three secretion needle.
Authors: Poyraz, O. / Schmidt, H. / Seidel, K. / Delissen, F. / Ader, C. / Tenenboim, H. / Goosmann, C. / Laube, B. / Thunemann, A.F. / Zychlinsky, A. / Baldus, M. / Lange, A. / Griesinger, C. / Kolbe, M.
History
DepositionMar 9, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 18, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _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: Protein prgI


Theoretical massNumber of molelcules
Total (without water)9,0911
Polymers9,0911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein prgI


Mass: 9091.037 Da / Num. of mol.: 1 / Mutation: V68A, V70A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SL1344 / Gene: prgI, STM2873 / Variant: enterica serovar / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P41784

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR solution structure of a functional full length PrgI mutant of the S. thyphimurium Type Three Secretion System
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HN(CA)CB
1423D HNCA
1523D CBCA(CO)NH
1623D HNCO
1723D (H)CCH-COSY
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11112D 1H-15N TROSY
11212D 1H-15N COCAINE
11332D 1H-15N TROSY
11432D 1H-15N COCAINE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 15N] PrgI*-1, 93% H2O/7% D2O93% H2O/7% D2O
20.3 mM [U-100% 13C; U-100% 15N] PrgI*-2, 93% H2O/7% D2O93% H2O/7% D2O
30.3 mM [U-100% 15N] PrgI*-3, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMPrgI*-1[U-100% 15N]1
0.3 mMPrgI*-2[U-100% 13C; U-100% 15N]2
0.3 mMPrgI*-3[U-100% 15N]3
Sample conditionsIonic strength: 20 / pH: 5.5 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004
Bruker AvanceBrukerAVANCE6005

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AtnosCandidHerrmann, Guntert and Wuthrichpeak picking
AtnosCandidHerrmann, Guntert and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: XPLOR-NIH simulated annealing using 36 RDCs
NMR constraintsNOE constraints total: 837 / NOE intraresidue total count: 262 / NOE long range total count: 88 / NOE medium range total count: 188 / NOE sequential total count: 299
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.42 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25 / Maximum torsion angle constraint violation: 4.04 ° / Maximum upper distance constraint violation: 0.4 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.03 Å / Distance rms dev error: 0.001 Å

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