[English] 日本語
Yorodumi- PDB-2e29: Solution structure of the GUCT domain from human ATP-dependent RN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2.0E+29 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the GUCT domain from human ATP-dependent RNA helicase DDX50, DEAD box protein 50 | ||||||
Components | ATP-dependent RNA helicase DDX50 | ||||||
Keywords | HYDROLASE / ATP binding / Helicase / Nuclear protein / Nucleotide-binding / RNA-binding / GUCT domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information RNA helicase activity / RNA helicase / nucleolus / RNA binding / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Ohnishi, S. / Paakkonen, K. / Guntert, P. / Sato, M. / Koshiba, S. / Harada, T. / Watanabe, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Solution structure of the GUCT domain from human RNA helicase II/Gubeta reveals the RRM fold, but implausible RNA interactions Authors: Ohnishi, S. / Paakkonen, K. / Koshiba, S. / Tochio, N. / Sato, M. / Kobayashi, N. / Harada, T. / Watanabe, S. / Muto, Y. / Guntert, P. / Tanaka, A. / Kigawa, T. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2e29.cif.gz | 541.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2e29.ent.gz | 455.2 KB | Display | PDB format |
PDBx/mmJSON format | 2e29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e29_validation.pdf.gz | 355.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2e29_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 2e29_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 2e29_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/2e29 ftp://data.pdbj.org/pub/pdb/validation_reports/e2/2e29 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 10149.377 Da / Num. of mol.: 1 / Fragment: GUCT domain, residues 8-92 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX50 / Plasmid: P060403-01 / Production host: Cell-free protein synthesis References: UniProt: Q9BQ39, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 0.9mM protein U-15N,13C; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics, restrained molecular dynamics Software ordinal: 1 Details: HNN and CACO RDC data, obtained from the Pf1 phage system, were used in the torsion angle dynamics calculation. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |