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- PDB-2lpz: Atomic model of the Type-III Secretion System Needle -

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Basic information

Entry
Database: PDB / ID: 2lpz
TitleAtomic model of the Type-III Secretion System Needle
ComponentsProtein prgI
KeywordsTRANSPORT PROTEIN / type three secretion system / filament / needle / helical assembly
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 enterica subsp. enterica serovar Typhimurium (bacteria)
MethodSOLID-STATE NMR / Monte Carlo, gradient-based optimization
Model detailslowest energy, model 1
AuthorsLoquet, A. / Sgourakis, N.G. / Gupta, R. / Giller, K. / Riedel, D. / Goosmann, C. / Griesinger, C. / Kolbe, M.G. / Baker, D. / Becker, S. / Lange, A.
CitationJournal: Nature / Year: 2012
Title: Atomic model of the type III secretion system needle.
Authors: Loquet, A. / Sgourakis, N.G. / Gupta, R. / Giller, K. / Riedel, D. / Goosmann, C. / Griesinger, C. / Kolbe, M. / Baker, D. / Becker, S. / Lange, A.
History
DepositionFeb 21, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Refinement description
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein prgI
B: Protein prgI
C: Protein prgI
D: Protein prgI
E: Protein prgI
F: Protein prgI
G: Protein prgI
H: Protein prgI
I: Protein prgI
J: Protein prgI
K: Protein prgI
L: Protein prgI
M: Protein prgI
N: Protein prgI
O: Protein prgI
P: Protein prgI
Q: Protein prgI
R: Protein prgI
S: Protein prgI
T: Protein prgI
U: Protein prgI
V: Protein prgI
W: Protein prgI
X: Protein prgI
Y: Protein prgI
Z: Protein prgI
a: Protein prgI
b: Protein prgI
c: Protein prgI


Theoretical massNumber of molelcules
Total (without water)257,08129
Polymers257,08129
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)10 / 1000000target function
RepresentativeModel #1lowest energy

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Components

#1: Protein ...
Protein prgI


Mass: 8864.868 Da / Num. of mol.: 29
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: prgI, STM2873 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P41784

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
Details: Atomic model of the Type III Secretion System Needle
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-13C PAIN-CP
121PDSD
13215N-13C PAIN-CP
142PDSD
15315N-13C PAIN-CP
163PDSD
17415N-13C PAIN-CP
184PDSD

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.1 mM [U-100% 13C; U-100% 15N] PrgI protein, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution20.1 mM [100% 1-13C glucose; U-100% 15N] PrgI protein, 90% H2O/10% D2Osample_290% H2O/10% D2O
solution30.1 mM [100% 2-13C glucose; U-100% 15N] PrgI protein, 90% H2O/10% D2Osample_390% H2O/10% D2O
solution40.1 mM [50% 1-13C glucose; 50% 2-13C glucose; U-100% 15N] PrgI protein, 90% H2O/10% D2Osample_490% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMPrgI protein[U-100% 13C; U-100% 15N]1
0.1 mMPrgI protein[100% 1-13C glucose; U-100% 15N]2
0.1 mMPrgI protein[100% 2-13C glucose; U-100% 15N]3
0.1 mMPrgI protein[50% 1-13C glucose; 50% 2-13C glucose; U-100% 15N]4
Sample conditionsIonic strength: 0 / pH: 7.5 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8502

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Processing

NMR software
NameVersionDeveloperClassification
Rosetta3.4Leaver-Fay, A. et al.structure calculations
CcpNmrCCPNdata analysis
Rosetta3.4Leaver-Fay, A. et al.refinement
RefinementMethod: Monte Carlo, gradient-based optimization / Software ordinal: 3
Details: Monte-Carlo and gradient-based refinement in torsion angle space of the rigid body, backbone and sidechain degrees of freedom
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1000000 / Conformers submitted total number: 10

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