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Yorodumi- PDB-1wh5: Solution structure of homeobox domain of Arabidopsisthaliana zinc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wh5 | ||||||
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Title | Solution structure of homeobox domain of Arabidopsisthaliana zinc finger homeobox family protein | ||||||
Components | ZF-HD homeobox family protein | ||||||
Keywords | DNA BINDING PROTEIN / homeobox / structural genomics / ZF-HD homeobox family protein / zinc finger homeobox family protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of gibberellin biosynthetic process / seed maturation / transcription cis-regulatory region binding / regulation of DNA-templated transcription / protein homodimerization activity / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Kaneno, D. / Tochio, N. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of homeobox domain of Arabidopsisthaliana zinc finger homeobox family protein Authors: Kaneno, D. / Tochio, N. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wh5.cif.gz | 484.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wh5.ent.gz | 403.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wh5_validation.pdf.gz | 347.6 KB | Display | wwPDB validaton report |
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Full document | 1wh5_full_validation.pdf.gz | 484.2 KB | Display | |
Data in XML | 1wh5_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 1wh5_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/1wh5 ftp://data.pdbj.org/pub/pdb/validation_reports/wh/1wh5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8904.975 Da / Num. of mol.: 1 / Fragment: homeobox domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA RAFL09-18-O11 / Plasmid: P030107-56 / References: UniProt: Q9FKP8 |
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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: 1.1mM homeobox domain U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 6.0 / 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 AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |