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- PDB-2k9n: Solution NMR structure of the R2R3 DNA binding domain of Myb1 pro... -

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Basic information

Entry
Database: PDB / ID: 2k9n
TitleSolution NMR structure of the R2R3 DNA binding domain of Myb1 protein from protozoan parasite Trichomonas vaginalis
ComponentsMYB24
KeywordsDNA BINDING PROTEIN / Myb1 / R2R3 Domain / DNA-binding / Nucleus
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Myb-like domain profile. / Myb-like DNA-binding domain / Myb-type HTH DNA-binding domain profile. / Myb domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesTrichomonas vaginalis (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsLou, Y. / Wei, S. / Rajasekaran, M. / Chou, C. / Hsu, H. / Tai, J. / Chen, C.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis.
Authors: Lou, Y.C. / Wei, S.Y. / Rajasekaran, M. / Chou, C.C. / Hsu, H.M. / Tai, J.H. / Chen, C.
History
DepositionOct 19, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / 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
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYB24


Theoretical massNumber of molelcules
Total (without water)13,2181
Polymers13,2181
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein MYB24


Mass: 13218.242 Da / Num. of mol.: 1 / Fragment: Myb1 R2R3 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58HP2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D 1H-15N NOESY
1623D 1H-13C NOESY
1713D HN(CA)CO
1823D (H)CCH-TOCSY
1913D C(CO)NH
11013D HBHA(CO)NH
11112D 1H-15N HxNOE

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium chloride, 20 mM sodium phosphate, 5 mM sodium azide, 20 mM beta-mercaptoethanol, 90% H2O/10% D2O90% H2O/10% D2O
250 mM sodium chloride, 20 mM sodium phosphate, 5 mM sodium azide, 20 mM beta-mercaptoethanol, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMsodium chloride1
20 mMsodium phosphate1
5 mMsodium azide1
20 mMbeta-mercaptoethanol1
50 mMsodium chloride2
20 mMsodium phosphate2
5 mMsodium azide2
20 mMbeta-mercaptoethanol2
Sample conditionsIonic strength: 0.17 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRViewJ8Johnson, One Moon Scientificchemical shift assignment
NMRViewJ8Johnson, One Moon Scientificdata analysis
NMRViewJ8Johnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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