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- PDB-5n7y: Solution structure of B. subtilis Sigma G inhibitor CsfB -

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Basic information

Entry
Database: PDB / ID: 5n7y
TitleSolution structure of B. subtilis Sigma G inhibitor CsfB
ComponentsAnti-sigma-G factor Gin
KeywordsTRANSCRIPTION / Zinc-finger / dimer / CsfB / Sigma G inhibitor
Function / homologyAnti-sigma-G factor Gin / Inhibitor of sigma-G Gin / sporulation resulting in formation of a cellular spore / metal ion binding / Anti-sigma-G factor Gin
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMartinez-Lumbreras, S. / Alfano, C. / Atkinson, A. / Isaacson, R.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Structure / Year: 2018
Title: Structural and Functional Insights into Bacillus subtilis Sigma Factor Inhibitor, CsfB.
Authors: Martinez-Lumbreras, S. / Alfano, C. / Evans, N.J. / Collins, K.M. / Flanagan, K.A. / Atkinson, R.A. / Krysztofinska, E.M. / Vydyanath, A. / Jackter, J. / Fixon-Owoo, S. / Camp, A.H. / Isaacson, R.L.
History
DepositionFeb 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 21, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_struct_conn_angle / pdbx_validate_close_contact
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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_representative.conformer_id / _pdbx_nmr_sample_details.contents / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.PDB_model_num
Revision 2.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-sigma-G factor Gin
C: Anti-sigma-G factor Gin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3924
Polymers11,2612
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2240 Å2
ΔGint-27 kcal/mol
Surface area6090 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Anti-sigma-G factor Gin / Protein CsfB


Mass: 5630.390 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: csfB, gin, yaaM, BSU00240 / Production host: Escherichia coli (E. coli) / References: UniProt: P37534
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HBHA(CO)NH
161isotropic13D HNCO
171isotropic13D (H)CCH-TOCSY
181isotropic13D 1H-15N NOESY
191isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-13C NOESY aromatic
1102isotropic23D filtered/edited 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N] CsfB-labelled, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
solution20.5 mM [U-100% 13C; U-100% 15N] CsfB-labelled, 0.5 mM CsfB, 90% H2O/10% D2Omixed_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCsfB-labelled[U-100% 13C; U-100% 15N]1
0.5 mMCsfB-labelled[U-100% 13C; U-100% 15N]2
0.5 mMCsfBnatural abundance2
Sample conditionsDetails: 50 mM HEPES, 250 mM NaCl, 250 uM TCEP / Ionic strength: 250 mM / Label: buffer / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE9502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.4CCPNchemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
TALOS+Cornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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