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- PDB-5tmx: Solution Structure of SinI, antagonist to the master biofilm-regu... -

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Basic information

Entry
Database: PDB / ID: 5tmx
TitleSolution Structure of SinI, antagonist to the master biofilm-regulator SinR in Bacillus subtilis
ComponentsProtein SinI
KeywordsTRANSCRIPTION REGULATOR / sporulation / repressor / biofilm
Function / homologySinR repressor/SinI anti-repressor, dimerisation domain / SinR repressor/SinI anti-repressor, dimerisation domain superfamily / Anti-repressor SinI / Sin domain profile. / protein dimerization activity / regulation of DNA-templated transcription / Protein SinI
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDraughn, G.L. / Bobay, B.G. / Stowe, S.D. / Thompson, R.J. / Cavanagh, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1-GM055769 United States
CitationJournal: J.Mol.Biol. / Year: 2019
Title: The Solution Structures and Interaction of SinR and SinI: Elucidating the Mechanism of Action of the Master Regulator Switch for Biofilm Formation in Bacillus subtilis.
Authors: Milton, M.E. / Draughn, G.L. / Bobay, B.G. / Stowe, S.D. / Olson, A.L. / Feldmann, E.A. / Thompson, R.J. / Myers, K.H. / Santoro, M.T. / Kearns, D.B. / Cavanagh, J.
History
DepositionOct 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein SinI
B: Protein SinI


Theoretical massNumber of molelcules
Total (without water)14,3682
Polymers14,3682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2670 Å2
ΔGint-20 kcal/mol
Surface area12270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy
DetailsDimer as determined by gel filtration

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Components

#1: Protein Protein SinI


Mass: 7184.149 Da / Num. of mol.: 2 / Fragment: residues 1-57
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sinI, BSU24600 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23308

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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
122isotropic12D 1H-13C HSQC
132isotropic13D HNCA
162isotropic13D HN(CO)CA
142isotropic13D HN(CA)CB
1122isotropic13D CBCA(CO)NH
152isotropic13D HNCO
172isotropic13D HN(CA)CO
182isotropic13D 1H-15N TOCSY
192isotropic13D C(CO)NH
1101isotropic13D 1H-15N NOESY
1113isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-15N] SinI, 20 mM MES, 200 mM sodium chloride, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution31 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 100% D2O15N_13C_D2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSinI[U-15N]1
20 mMMESnatural abundance1
200 mMsodium chloridenatural abundance1
1 mMSinI[U-13C; U-15N]2
20 mMMESnatural abundance2
200 mMNaClnatural abundance2
1 mMSinI[U-13C; U-15N]3
20 mMMESnatural abundance3
200 mMNaClnatural abundance3
Sample conditionsIonic strength: 200 mM / Label: conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 3
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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