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Yorodumi- PDB-1wew: Solution structure of PHD domain in DNA-binding family protein AA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wew | ||||||
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Title | Solution structure of PHD domain in DNA-binding family protein AAM98074 | ||||||
Components | DNA-binding family protein | ||||||
Keywords | DNA BINDING PROTEIN / structural genomics / PHD domain / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of systemic acquired resistance / detection of phosphate ion / regulation of salicylic acid metabolic process / shoot regeneration / regulation of nitrate assimilation / regulation of response to water deprivation / response to freezing / pollen tube guidance / regulation of abscisic acid-activated signaling pathway / heat acclimation ...negative regulation of systemic acquired resistance / detection of phosphate ion / regulation of salicylic acid metabolic process / shoot regeneration / regulation of nitrate assimilation / regulation of response to water deprivation / response to freezing / pollen tube guidance / regulation of abscisic acid-activated signaling pathway / heat acclimation / negative regulation of flower development / plant ovule development / unidimensional cell growth / embryo sac development / SUMO ligase activity / response to water deprivation / cellular response to phosphate starvation / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / regulation of growth / protein sumoylation / developmental growth / defense response / nuclear speck / cell division / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | He, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of PHD domain in DNA-binding family protein AAM98074 Authors: He, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wew.cif.gz | 443.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wew.ent.gz | 367.8 KB | Display | PDB format |
PDBx/mmJSON format | 1wew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/1wew ftp://data.pdbj.org/pub/pdb/validation_reports/we/1wew | HTTPS FTP |
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-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: 8419.436 Da / Num. of mol.: 1 / Fragment: PHD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: Cell free protein synthesis / Gene: RAFL09-09-B06 / Plasmid: P030408-04 / References: UniProt: Q680Q4 |
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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: 0.8mM U-15,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 0.1mM ZnCl2; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 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: 700 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, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |