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- PDB-2lnv: Solution structure of GspC-HR of typeII secretion system -

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Basic information

Entry
Database: PDB / ID: 2lnv
TitleSolution structure of GspC-HR of typeII secretion system
ComponentsGeneral secretion pathway protein C
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / protein processing / membrane => GO:0016020 / plasma membrane
Similarity search - Function
SH3 type barrels. - #830 / Type II secretion system protein GspC / Bacterial type II secretion system protein C signature. / Type II secretion system protein GspC, N-terminal / Type II secretion system protein C / PDZ superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Type II secretion system protein C
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 10
AuthorsGu, S. / Kelly, G. / Pickersgill, R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Solution Structure of Homology Region (HR) Domain of Type II Secretion System.
Authors: Gu, S. / Kelly, G. / Wang, X. / Frenkiel, T. / Shevchik, V.E. / Pickersgill, R.W.
History
DepositionJan 5, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General secretion pathway protein C


Theoretical massNumber of molelcules
Total (without water)11,1381
Polymers11,1381
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein General secretion pathway protein C / Pectic enzymes secretion protein outC


Mass: 11138.301 Da / Num. of mol.: 1 / Fragment: UNP residues 77-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (bacteria) / Strain: 3937 / Gene: outC, Dda3937_02414 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01564

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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 HN(CA)CB
1313D CBCA(CO)NH
1413D 1H-15N TOCSY
1513D 1H-15N NOESY
1613D HNHA
1713D HNCO
1812D 1H-13C HSQC
1913D HBHA(CO)NH
11013D 1H-13C NOESY aliphatic
11113D HNCA
11212D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: D2O-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0 / pH: 7.0 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance7001
Bruker AvanceBrukerAvance6002
Varian INOVAVarianINOVA8003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
TALOSCornilescu, Delaglio and Baxdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TOPSPINBruker Biospincollection
VNMRVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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