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Yorodumi- PDB-1ul4: Solution structure of the DNA-binding domain of squamosa promoter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ul4 | ||||||
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Title | Solution structure of the DNA-binding domain of squamosa promoter binding protein-like 4 | ||||||
Components | squamosa promoter binding protein-like 4 | ||||||
Keywords | DNA BINDING PROTEIN / Transcription factor / SBP / Flower development / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of vegetative phase change / flower development / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Yamasaki, K. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. Authors: Yamasaki, K. / Kigawa, T. / Inoue, M. / Tateno, M. / Yamasaki, T. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Nunokawa, E. / Ishizuka, Y. / Terada, T. / Shirouzu, M. / Osanai, T. / ...Authors: Yamasaki, K. / Kigawa, T. / Inoue, M. / Tateno, M. / Yamasaki, T. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Nunokawa, E. / Ishizuka, Y. / Terada, T. / Shirouzu, M. / Osanai, T. / Tanaka, A. / Seki, M. / Shinozaki, K. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ul4.cif.gz | 522.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ul4.ent.gz | 434.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ul4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ul4_validation.pdf.gz | 346.1 KB | Display | wwPDB validaton report |
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Full document | 1ul4_full_validation.pdf.gz | 472.2 KB | Display | |
Data in XML | 1ul4_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 1ul4_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/1ul4 ftp://data.pdbj.org/pub/pdb/validation_reports/ul/1ul4 | 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: 10621.970 Da / Num. of mol.: 1 / Fragment: DNA-binding domain (SBP domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: cell-free synthesis / Gene: SPL4 / Plasmid: pCR2.1 / References: UniProt: Q9S7A9 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.02mM ZNCL2 |
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Sample conditions | Ionic strength: 20mM KPi, 300mM KCl / pH: 6 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |