+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ugg | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of unmodified E. coli tRNA(Asp) | |||||||||||||||
![]() | tRNAasp | |||||||||||||||
![]() | RNA / tRNA RNA unmodified | |||||||||||||||
Function / homology | : / RNA / RNA (> 10)![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Chan, C.W. / Mondragon, A. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs. Authors: Chan, C.W. / Badong, D. / Rajan, R. / Mondragon, A. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 92.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 69.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 247.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 247.9 KB | Display | |
Data in XML | ![]() | 940 B | Display | |
Data in CIF | ![]() | 2.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ugiC ![]() 6ugjC ![]() 1ehzS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 24815.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.36 % Description: Clusters of arrow-like crystals. Single crystals excised from cluster. |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 uL 20 mg/ml E. coli tRNA(Asp) + 2 uL equilibration solution (50 mM sodium cacodylate, pH 7.5, 30% MPD, 10 mM spermine tetrahydrochloride, 300 mM sodium chloride, 300 mM potassium chloride) ...Details: 2 uL 20 mg/ml E. coli tRNA(Asp) + 2 uL equilibration solution (50 mM sodium cacodylate, pH 7.5, 30% MPD, 10 mM spermine tetrahydrochloride, 300 mM sodium chloride, 300 mM potassium chloride) + 0.5 uL 0.25% w/v p-coumaric acid, 0.25% w/v phenylurea, 0.25% w/v poly(3-hydroxybutyric acid), 0.25% w/v sulfaguanidine, 0.02 M sodium HEPES, pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: Crystals were flash frozen directly in mother liquor with liquid nitrogen Serial crystal experiment: N | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2017 / Details: Monochromator | |||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.0782 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 1.95→48.62 Å / Num. obs: 35638 / % possible obs: 94 % / Redundancy: 30 % / CC1/2: 0.992 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.029 / Rrim(I) all: 0.158 / Net I/σ(I): 15.8 | |||||||||||||||
Reflection shell | Resolution: 1.95→2.056 Å / Redundancy: 33.7 % / Rmerge(I) obs: 2.683 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 55102 / CC1/2: 0.488 / Rpim(I) all: 0.468 / Rrim(I) all: 2.724 / % possible all: 50.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1EHZ Resolution: 1.95→48.62 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.442 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.035 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.64 Å2 / Biso mean: 50.999 Å2 / Biso min: 22.58 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→48.62 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|