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- PDB-2mhj: Solution structure of TpsB4 N-terminal POTRA domain from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 2mhj
TitleSolution structure of TpsB4 N-terminal POTRA domain from Pseudomonas aeruginosa
ComponentsTpsB4 protein
KeywordsPROTEIN TRANSPORT / two partner secreation / TPS / T5SS / biofilm / secretion / protease / POTRA / Omp85
Function / homology
Function and homology information


type V protein secretion system complex / protein secretion by the type V secretion system / protein transmembrane transporter activity
Similarity search - Function
Haemolysin activator HlyB, C-terminal / Haemolysin secretion/activation protein ShlB/FhaC/HecB / Polypeptide-transport-associated, ShlB-type / POTRA domain, ShlB-type / membrane protein fhac / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsGarnett, J.A. / Matthews, S.J.
CitationJournal: Protein Sci. / Year: 2015
Title: Structure-function analysis reveals that the Pseudomonas aeruginosa Tps4 two-partner secretion system is involved in CupB5 translocation.
Authors: Garnett, J.A. / Muhl, D. / Douse, C.H. / Hui, K. / Busch, A. / Omisore, A. / Yang, Y. / Simpson, P. / Marchant, J. / Waksman, G. / Matthews, S. / Filloux, A.
History
DepositionNov 25, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TpsB4 protein


Theoretical massNumber of molelcules
Total (without water)10,7641
Polymers10,7641
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TpsB4 protein


Mass: 10764.116 Da / Num. of mol.: 1 / Fragment: POTRA domain 1 (UNP residues 55-134)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA4540 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: Q9HVN7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HN(CO)CA
1813D H(CCO)NH
1923D (H)CCH-TOCSY
11023D 1H-13C NOESY aromatic
11113D 1H-15N NOESY
11213D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] TpsB4, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] TpsB4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTpsB4-1[U-13C; U-15N]1
1 mMTpsB4-2[U-13C; U-15N]2
Sample conditionsIonic strength: 0.2 / pH: 7.0 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1818
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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