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- PDB-2kko: Solution NMR structure of the homodimeric winged helix-turn-helix... -

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Basic information

Entry
Database: PDB / ID: 2kko
TitleSolution NMR structure of the homodimeric winged helix-turn-helix DNA-binding domain (fragment 1-100) Mb0332 from Mycobacterium bovis, a possible ArsR-family transcriptional regulator. Northeast Structural Genomics Consortium Target MbR242E.
ComponentsPOSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY ARSR-FAMILY)
KeywordsDNA BINDING PROTEIN / NESG / DNA-BINDING / TRANSCRIPTION REGULATION / TRANSCRIPTIONAL REGULATOR / wHTH / HOMODIMER / winged helix-turn-helix / Transcription / Transferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesMycobacterium bovis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRamelot, T.A. / Cort, J.R. / Wang, D. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. ...Ramelot, T.A. / Cort, J.R. / Wang, D. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the homodimeric winged helix-turn-helix DNA-binding domain (fragment 1-100) Mb0332 from Mycobacterium bovis, a possible ArsR-family transcriptional regulator. ...Title: Solution NMR structure of the homodimeric winged helix-turn-helix DNA-binding domain (fragment 1-100) Mb0332 from Mycobacterium bovis, a possible ArsR-family transcriptional regulator. Northeast Structural Genomics Consortium Target MbR242E.
Authors: Ramelot, T.A. / Cort, J.R. / Wang, D. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Swapna, G. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 26, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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: POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY ARSR-FAMILY)
B: POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY ARSR-FAMILY)


Theoretical massNumber of molelcules
Total (without water)23,4932
Polymers23,4932
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY ARSR-FAMILY)


Mass: 11746.304 Da / Num. of mol.: 2 / Fragment: HTH arsR-type DNA binding domain residues 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (bacteria) / Gene: Mb0332 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q7U294

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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 1H-15N NOESY
1413D 1H-13C NOESY
1513D HNCO
1613D HNCA
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D C(CO)NH
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY
11213D (H)CCH-COSY
11322D 1H-13C HSQC
11413D 1H-13C NOESY arom
11533D CN filt 1H-13C NOESY
11632D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM MES, 200 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 1.1 mM [U-100% 13C; U-100% 15N] protein, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
220 mM MES, 200 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 0.8 mM [U-5% 13C; U-100% 15N] protein, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
320 mM MES, 200 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 0.5 mM [U-100% 13C; U-100% 15N] protein, 50 uM DSS, .5 mM protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMES1
200 mMsodium chloride1
10 mMDTT1
0.02 %sodium azide1
1.1 mMprotein[U-100% 13C; U-100% 15N]1
50 uMDSS1
20 mMMES2
200 mMsodium chloride2
10 mMDTT2
0.02 %sodium azide2
0.8 mMprotein[U-5% 13C; U-100% 15N]2
50 uMDSS2
20 mMMES3
200 mMsodium chloride3
10 mMDTT3
0.02 %sodium azide3
.5 mMprotein-1[U-100% 13C; U-100% 15N]3
50 uMDSS3
.5 mMprotein-23
Sample conditionsIonic strength: 200 / pH: 6 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.3Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure validation
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PDBStat) R. Tejero, G.T. Montelionedata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS water refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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