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- PDB-6i2o: Solution NMR structure of PilE1 from Streptococcus sanguinis -

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Basic information

Entry
Database: PDB / ID: 6i2o
TitleSolution NMR structure of PilE1 from Streptococcus sanguinis
ComponentsType IV pilin PilE1
KeywordsPROTEIN FIBRIL / TYPE IV PILIN / PILIN / PILUS
Function / homologyestablishment of competence for transformation / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / membrane / Type IV pilin PilE1
Function and homology information
Biological speciesStreptococcus sanguinis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBerry, J.L. / Xu, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Global biochemical and structural analysis of the type IV pilus from the Gram-positive bacteriumStreptococcus sanguinis.
Authors: Berry, J.L. / Gurung, I. / Anonsen, J.H. / Spielman, I. / Harper, E. / Hall, A.M.J. / Goosens, V.J. / Raynaud, C. / Koomey, M. / Biais, N. / Matthews, S. / Pelicic, V.
History
DepositionNov 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type IV pilin PilE1


Theoretical massNumber of molelcules
Total (without water)12,0841
Polymers12,0841
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6340 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Type IV pilin PilE1


Mass: 12084.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis (bacteria) / Gene: pilE1, SSV_2241 / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: A0A0B7GU52

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HBHA(CO)NH
121isotropic13D HN(CA)CB
131isotropic13D HNCO
141isotropic13D HN(CO)CA
151isotropic13D CBCA(CO)NH
181isotropic13D H(CCO)NH
171isotropic13D (H)CCH-TOCSY
191isotropic12D 1H-15N HSQC
1101isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution / Contents: 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O / Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 750 nM / Component: PilE1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue, Nilgesstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
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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