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- PDB-2jmw: Structure of DNA-Binding Domain of Arabidopsis GT-1 -

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Basic information

Entry
Database: PDB / ID: 2jmw
TitleStructure of DNA-Binding Domain of Arabidopsis GT-1
ComponentsDNA binding protein GT-1
KeywordsDNA BINDING PROTEIN / DNA-binding domain / Phosphorylation
Function / homology
Function and homology information


sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding / nucleus
Similarity search - Function
Myb/SANT-like DNA-binding domain 4 / Myb/SANT-like DNA-binding domain / Myb-like domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Trihelix transcription factor GT-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsNagata, T. / Niyada, E. / Noto, K. / Ikeda, Y. / Yamamoto, Y. / Uesugi, S. / Murata, J. / Hiratsuka, K. / Katahira, M.
CitationJournal: Proteins / Year: 2010
Title: Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: mechanism for an increase in DNA-binding affinity through phosphorylation.
Authors: Nagata, T. / Niyada, E. / Fujimoto, N. / Nagasaki, Y. / Noto, K. / Miyanoiri, Y. / Murata, J. / Hiratsuka, K. / Katahira, M.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA binding protein GT-1


Theoretical massNumber of molelcules
Total (without water)10,3541
Polymers10,3541
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 #1lowest energy

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Components

#1: Protein DNA binding protein GT-1 / Hypothetical protein At1g13450


Mass: 10353.913 Da / Num. of mol.: 1 / Fragment: residues 81-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: T6J4.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FX53

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C, U-100% 15N] GT-1, 20 mM sodium phosphate, 100 mM sodium chloride, 10 mM [U-100% 2H] DTT, 1 mM sodium azide, 1 mM DSS, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.60 mMGT-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate1
100 mMsodium chloride1
10 mMDTT[U-100% 2H]1
1 mMsodium azide1
1 mMDSS1
Sample conditionsIonic strength: 120 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
KUJIRA0.982Kobayashichemical shift assignment
KUJIRA0.982Kobayashidata analysis
KUJIRA0.982Kobayashipeak picking
NMRView5.0.4Johnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XwinNMR3.5Bruker Biospincollection
CYANA2.0.17Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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