[English] 日本語
Yorodumi- PDB-2k4c: tRNAPhe-based homology model for tRNAVal refined against base N-H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k4c | ||||||
---|---|---|---|---|---|---|---|
Title | tRNAPhe-based homology model for tRNAVal refined against base N-H RDCs in two media and SAXS data | ||||||
Components | 76-MER | ||||||
Keywords | RNA / tRNAVal / RDC / SAXS / NCS | ||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / SOLUTION SCATTERING / simulated annealing, torsion angle dynamics | ||||||
Authors | Grishaev, A. / Ying, J. / Canny, M.D. / Pardi, A. / Bax, A. | ||||||
Citation | Journal: J.Biomol.Nmr / Year: 2008 Title: Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. Authors: Grishaev, A. / Ying, J. / Canny, M.D. / Pardi, A. / Bax, A. #1: Journal: J.Biomol.NMR / Year: 2007 Title: Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field Authors: Ying, J. / Grishaev, A. / Latham, M. / Pardi, A. / Bax, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2k4c.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2k4c.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 2k4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k4c_validation.pdf.gz | 304.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2k4c_full_validation.pdf.gz | 304.4 KB | Display | |
Data in XML | 2k4c_validation.xml.gz | 2 KB | Display | |
Data in CIF | 2k4c_validation.cif.gz | 2.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/2k4c ftp://data.pdbj.org/pub/pdb/validation_reports/k4/2k4c | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: RNA chain | Mass: 24483.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Description: sample is uniformly 15N labeled / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: GenBank: 1845291569 |
---|
-Experimental details
-Experiment
Experiment |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||||||||||
Sample conditions |
|
-Data collection
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: tRNAVal solution structure is obtained by refinement of the tRNAPhe based homology model against RDC data (base N-H RDCs) from Pf1 and self-alignment (MSA), and SAXS data. Totals of 24 Pf1 ...Details: tRNAVal solution structure is obtained by refinement of the tRNAPhe based homology model against RDC data (base N-H RDCs) from Pf1 and self-alignment (MSA), and SAXS data. Totals of 24 Pf1 RDCs and 20 MSA RDcs were fitted. During the refinement, the local geometry was kept close to the tRNAPhe based homology model using a set of non-crystallographic symmetry restraint terms. The NCS potentials included: 70 sequential i/i+1 terms and 34 additional terms for base pairs and triplets. The experimental SAXS data between q=0.03 and 0.35 A^-1 were fitted as well. | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 3 / Conformers submitted total number: 1 |