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- PDB-2krf: NMR solution structure of the DNA binding domain of Competence pr... -

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Basic information

Entry
Database: PDB / ID: 2krf
TitleNMR solution structure of the DNA binding domain of Competence protein A
ComponentsTranscriptional regulatory protein comA
KeywordsTRANSCRIPTION / Activator / Competence / DNA-binding / Transcription regulation / Two-component regulatory system
Function / homology
Function and homology information


establishment of competence for transformation / phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulatory protein ComA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHobbs, C.A. / Bobay, B.G. / Thompson, R.J. / Perego, M. / Cavanagh, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: NMR solution structure and DNA-binding model of the DNA-binding domain of competence protein A.
Authors: Hobbs, C.A. / Bobay, B.G. / Thompson, R.J. / Perego, M. / Cavanagh, J.
History
DepositionDec 16, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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 8, 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: Transcriptional regulatory protein comA
B: Transcriptional regulatory protein comA


Theoretical massNumber of molelcules
Total (without water)16,1702
Polymers16,1702
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional regulatory protein comA


Mass: 8085.142 Da / Num. of mol.: 2 / Fragment: residues 146-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU31680, comA, comA1, comAA / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: P14204

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HN(CO)CA
1813D H(CCO)NH
1923D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 2 mM EDTA, 1 mM [U-13C; U-15N] ComAC, 90% H2O/10% D2O90% H2O/10% D2O
225 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 2 mM EDTA, 1 mM [U-13C; U-15N] ComAC, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphate-11
100 mMsodium chloride-21
1 mMDTT-31
2 mMEDTA-41
1 mMComAC-5[U-13C; U-15N]1
25 mMsodium phosphate-62
100 mMsodium chloride-72
1 mMDTT-82
2 mMEDTA-92
1 mMComAC-10[U-13C; U-15N]2
Sample conditionspH: 6.5 / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
VnmrJVariancollection
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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