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- PDB-2kep: Solution structure of XcpT, the main component of the type 2 secr... -

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Basic information

Entry
Database: PDB / ID: 2kep
TitleSolution structure of XcpT, the main component of the type 2 secretion system of Pseudomonas aeruginosa
ComponentsGeneral secretion pathway protein G
KeywordsTRANSPORT PROTEIN / Methylation / Transport
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Type II secretion system protein GspG / Type II secretion system protein GspG, C-terminal / Type II secretion system (T2SS), protein G / Glycoprotein, Type 4 Pilin / Bacterial general secretion pathway protein G-type pilin / Glycoprotein, Type 4 Pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II secretion system core protein G
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAlphonse, S. / Durand, E. / Douzi, B. / Darbon, H. / Filloux, A. / Voulhoux, R. / Bernard, C.
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Structure of the Pseudomonas aeruginosa XcpT pseudopilin, a major component of the type II secretion system
Authors: Alphonse, S. / Durand, E. / Douzi, B. / Waegele, B. / Darbon, H. / Filloux, A. / Voulhoux, R. / Bernard, C.
History
DepositionFeb 2, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General secretion pathway protein G


Theoretical massNumber of molelcules
Total (without water)11,9571
Polymers11,9571
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)20 / 60structures with acceptable covalent geometry
RepresentativeModel #1fewest violations

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Components

#1: Protein General secretion pathway protein G / PilD-dependent protein pddA / XcpT


Mass: 11957.292 Da / Num. of mol.: 1 / Fragment: UNP residues 33-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3101, pddA, xcpT / Plasmid: peT22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pLysS(DE3) / References: UniProt: Q00514

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-1H TOCSY
2212D 1H-1H NOESY
1322D 1H-15N HSQC
1442D 1H-13C HSQC
1543D CBCA(CO)NH
1643D HNCO
1743D HNCA
1843D HN(CA)CB
1943D HBHA(CO)NH
11043D HN(CO)CA
11143D (H)CCH-TOCSY
11223D HNHA
11323D 1H-15N NOESY
11423D 1H-15N TOCSY
11543D HNHB
11643D HCACO
11732D 1H-15N HSQC
11832D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3mM XcpT, 50mM sodium phosphate, 150mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.9mM [U-15N] XcpT, 50mM sodium phosphate, 150mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
30.9mM [U-15N] XcpT, 100% D2O100% D2O
40.9mM [U-13C; U-15N] XcpT, 50mM sodium phosphate, 150mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMXcpT1
50 mMsodium phosphate1
150 mMsodium chloride1
0.9 mMXcpT[U-15N]2
50 mMsodium phosphate2
150 mMsodium chloride2
0.9 mMXcpT[U-15N]3
0.9 mMXcpT[U-13C; U-15N]4
50 mMsodium phosphate4
150 mMsodium chloride4
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17 ambient 290 K
27 ambiant 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
NMRView5.2.2.01Johnson, One Moon Scientificpeak picking
NMRView5.2.2.01Johnson, One Moon Scientificchemical shift assignment
NMRView5.2.2.01Johnson, One Moon Scientificdata analysis
TALOS3.851Cornilescu, Delaglio, Baxgeometry optimization
CYANA2.1Guntert, Mumenthaler, Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra, Clorerefinement
ProcheckNMR3.4Laskowski, MacArthurdata analysis
WHAT IF20080408-2247Vrienddata analysis
QUEEN1.1Nabuurs, Spronk, Krieger, Maassen, Vriend, Vuisterdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1113 / NOE intraresidue total count: 331 / NOE long range total count: 288 / NOE medium range total count: 173 / NOE sequential total count: 321 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 68 / Protein psi angle constraints total count: 77
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 60 / Conformers submitted total number: 20 / Representative conformer: 1

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