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- PDB-2l0k: NMR solution structure of a transcription factor SpoIIID in compl... -

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Basic information

Entry
Database: PDB / ID: 2l0k
TitleNMR solution structure of a transcription factor SpoIIID in complex with DNA
ComponentsStage III sporulation protein D
KeywordsTRANSCRIPTION / SpoIIID / NMR solution structure / DNA binding / Bacillus subtilis / Transcription factor
Function / homologySporulation stage III, transcriptional regulator SpoIIID / Stage III sporulation protein D / Transcription regulator, HTH DeoR-type, conserved site / DeoR-type HTH domain signature. / sporulation resulting in formation of a cellular spore / DNA-binding transcription factor activity / DNA binding / Stage III sporulation protein D
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsChen, B. / Himes, P. / Lu, Z. / Liu, A. / Yan, H. / Kroos, L.
CitationJournal: To be Published
Title: Novel Mode of DNA Binding by Bacterial Transcription Factor SpoIIID
Authors: Chen, B. / Himes, P. / Liu, Y. / Zhang, Y. / Lu, Z. / Liu, A. / Yan, H. / Kroos, L.
History
DepositionJul 8, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stage III sporulation protein D


Theoretical massNumber of molelcules
Total (without water)10,8261
Polymers10,8261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Stage III sporulation protein D / 14 kDa transcription factor


Mass: 10825.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: spoIIID, BSU36420 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / References: UniProt: P15281

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: SpoIIID is evolutionarily conserved in endospore-forming bacteria and it activates or represses many genes during sporulation of Bacillus subtilis. A SpoIIID monomer binds DNA with high ...Details: SpoIIID is evolutionarily conserved in endospore-forming bacteria and it activates or represses many genes during sporulation of Bacillus subtilis. A SpoIIID monomer binds DNA with high affinity and sequence specificity. SpoIIID has a helix-turn-helix domain with a novel C-terminal helical extension. The recognition helix of the helix-turn-helix domain interacts with the major groove of DNA and the C-terminal helical extension interacts with the adjacent minor groove of DNA. This novel and efficient mode of DNA binding might have evolved uniquely in endospore-forming bacteria to conserve biosynthetic capacity as resources dwindle during the starvation-induced sporulation process.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CO)CA
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 10 mM potassium phosphate-1, 100 mM sodium chloride-2, 15 mM sodium azide-3, 0.05 mM DSS-4, 5.5 M [U-100% 2H] D2O-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMpotassium phosphate-11
100 mMsodium chloride-21
15 mMsodium azide-31
0.05 mMDSS-41
5.5 MD2O-5[U-100% 2H]1
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichcollection
CYANA2.1Guntert, Mumenthaler and Wuthrichdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmchemical shift assignment
CYANA2.1Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmcollection
CYANA2.1Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmdata analysis
CYANA2.1Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmpeak picking
CYANA2.1Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmprocessing
CYANA2.1Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
CYANA2.1Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
CYANA2.1Accelrys Software Inc.chemical shift assignment
CYANA2.1Accelrys Software Inc.collection
CYANA2.1Accelrys Software Inc.data analysis
CYANA2.1Accelrys Software Inc.peak picking
CYANA2.1Accelrys Software Inc.processing
CYANA2.1Accelrys Software Inc.refinement
CYANA2.1Accelrys Software Inc.structure solution
CYANA2.1Koradi, Billeter and Wuthrichchemical shift assignment
CYANA2.1Koradi, Billeter and Wuthrichcollection
CYANA2.1Koradi, Billeter and Wuthrichdata analysis
CYANA2.1Koradi, Billeter and Wuthrichpeak picking
CYANA2.1Koradi, Billeter and Wuthrichprocessing
CYANA2.1Koradi, Billeter and Wuthrichrefinement
CYANA2.1Koradi, Billeter and Wuthrichstructure solution
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxcollection
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
CYANA2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
CYANA2.1Johnson, One Moon Scientificchemical shift assignment
CYANA2.1Johnson, One Moon Scientificcollection
CYANA2.1Johnson, One Moon Scientificdata analysis
CYANA2.1Johnson, One Moon Scientificpeak picking
CYANA2.1Johnson, One Moon Scientificprocessing
CYANA2.1Johnson, One Moon Scientificrefinement
CYANA2.1Johnson, One Moon Scientificstructure solution
CYANA2.1Laskowski and MacArthurchemical shift assignment
CYANA2.1Laskowski and MacArthurcollection
CYANA2.1Laskowski and MacArthurdata analysis
CYANA2.1Laskowski and MacArthurpeak picking
CYANA2.1Laskowski and MacArthurprocessing
CYANA2.1Laskowski and MacArthurrefinement
CYANA2.1Laskowski and MacArthurstructure solution
CYANA2.1Cornilescu, Delaglio and Baxchemical shift assignment
CYANA2.1Cornilescu, Delaglio and Baxcollection
CYANA2.1Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Cornilescu, Delaglio and Baxpeak picking
CYANA2.1Cornilescu, Delaglio and Baxprocessing
CYANA2.1Cornilescu, Delaglio and Baxrefinement
CYANA2.1Cornilescu, Delaglio and Baxstructure solution
CYANA2.1Bruker Biospinchemical shift assignment
CYANA2.1Bruker Biospincollection
CYANA2.1Bruker Biospindata analysis
CYANA2.1Bruker Biospinpeak picking
CYANA2.1Bruker Biospinprocessing
CYANA2.1Bruker Biospinrefinement
CYANA2.1Bruker Biospinstructure solution
CYANA2.1Varianchemical shift assignment
CYANA2.1Variancollection
CYANA2.1Variandata analysis
CYANA2.1Varianpeak picking
CYANA2.1Varianprocessing
CYANA2.1Varianrefinement
CYANA2.1Varianstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2194 / NOE intraresidue total count: 628 / NOE long range total count: 312 / NOE medium range total count: 621 / NOE sequential total count: 633 / Protein phi angle constraints total count: 66 / Protein psi angle constraints total count: 66
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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