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Yorodumi- PDB-2ebi: Arabidopsis GT-1 DNA-binding domain with T133D phosphomimetic mutation -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ebi | ||||||
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Title | Arabidopsis GT-1 DNA-binding domain with T133D phosphomimetic mutation | ||||||
Components | DNA binding protein GT-1 | ||||||
Keywords | DNA 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 | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS | ||||||
Authors | Nagata, T. / Noto, K. / Niyada, E. / Ikeda, Y. / Yamamoto, Y. / Uesugi, S. / Murata, J. / Hiratsuka, K. / Katahira, M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ebi.cif.gz | 560.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ebi.ent.gz | 472.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ebi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ebi_validation.pdf.gz | 341.3 KB | Display | wwPDB validaton report |
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Full document | 2ebi_full_validation.pdf.gz | 485.3 KB | Display | |
Data in XML | 2ebi_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 2ebi_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/2ebi ftp://data.pdbj.org/pub/pdb/validation_reports/eb/2ebi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10367.897 Da / Num. of mol.: 1 / Fragment: DNA-binding domain, residues 81-166 / Mutation: T133D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: T6J4.18 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9FX53 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.6mM PROTEIN U-15N,13C, 20mM phosphate buffer NA, 100mM NaCl, 10mM DTT, 1mM NaN3, 0.1% DSS, 95% H2O; 5% D2O Solvent system: 95% H2O/5% D2O |
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Sample conditions | Ionic strength: 120 mM / pH: 6 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |