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- PDB-6y1h: Major subunit ComGC from S. pneumoniae Com pseudopili -

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Basic information

Entry
Database: PDB / ID: 6y1h
TitleMajor subunit ComGC from S. pneumoniae Com pseudopili
ComponentsCompetence protein
KeywordsSTRUCTURAL PROTEIN / type IV filaments type IV pilin competence pseudopili mainly alpha orthogonal bundle
Function / homologyComG operon protein C / Bacterial general secretion pathway protein G-type pilin / establishment of competence for transformation / protein secretion by the type II secretion system / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / type II protein secretion system complex / Competence protein
Function and homology information
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSheppard, D. / Berry, J.L. / Matthews, S.J. / Pelicic, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/P022197/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold.
Authors: Sheppard, D. / Berry, J.L. / Denise, R. / Rocha, E.P.C. / Matthews, S. / Pelicic, V.
History
DepositionFeb 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Competence protein


Theoretical massNumber of molelcules
Total (without water)7,9491
Polymers7,9491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5170 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 Competence protein


Mass: 7948.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: cglC, spr1862 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DN88

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D CBCANH
141isotropic13D CBCA(CO)NH
151isotropic13D HNCA
161isotropic13D HNCO
171isotropic13D HN(CA)CO
181isotropic13D (H)CC(CO)NH
191isotropic13D CC(CO)NH
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D HBHA(CO)NH
1122isotropic12D IPAP HSQC
1133anisotropic12D IPAP HSQC
1141isotropic13D 15N NOESY
1151isotropic13D 13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.8 mM [U-100% 13C; U-100% 15N] ComGC, 25 mM NA Na2HPO4/NaH2PO4, 50 mM NA NaCl, 5 % NA D2O, 95% H2O/5% D2O15N_13C_sample95% H2O/5% D2O
solution20.5 mM [U-100% 15N] ComGC, 25 mM NA Na2HPO4/NaH2PO4, 50 mM NA NaCl, 5 % NA D2O, 95% H2O/5% D2O15N_isotropic_sample95% H2O/5% D2O
reverse micelle30.5 mM [U-100% 15N] ComGC, 25 mM NA Na2HPO4/NaH2PO4, 50 mM NA NaCl, 5 % NA D2O, 3.0 % NA PEG/hexanol, 95% H2O/5% D2O15N_aligned_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.8 mMComGC[U-100% 13C; U-100% 15N]1
25 mMNa2HPO4/NaH2PO4NA1
50 mMNaClNA1
5 %D2ONA1
0.5 mMComGC[U-100% 15N]2
25 mMNa2HPO4/NaH2PO4NA2
50 mMNaClNA2
5 %D2ONA2
0.5 mMComGC[U-100% 15N]3
25 mMNa2HPO4/NaH2PO4NA3
50 mMNaClNA3
5 %D2ONA3
3.0 %PEG/hexanolNA3
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz / Details: cryoprobe

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Processing

SoftwareName: THESEUS / Version: 3.3.0 / Classification: refinement
NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
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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