[English] 日本語
![](img/lk-miru.gif)
- PDB-5x6b: Crystal structure of SepCysE-SepCysS in complex with tRNACys from... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5x6b | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SepCysE-SepCysS in complex with tRNACys from Methanocaldococcus jannaschii | ||||||
![]() |
| ||||||
![]() | RNA BINDING PROTEIN/RNA / SepCysE / multidomain protein / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | ![]() O-phospho-L-seryl-tRNA:Cys-tRNA synthase / Sep-tRNA:Cys-tRNA synthase activity / translation Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, M. / Kato, K. / Yao, M. | ||||||
![]() | ![]() Title: Structural basis for tRNA-dependent cysteine biosynthesis Authors: Chen, M. / Kato, K. / Kubo, Y. / Tanaka, Y. / Liu, Y. / Long, F. / Whitman, W.B. / Lill, P. / Gatsogiannis, C. / Raunser, S. / Shimizu, N. / Shinoda, A. / Nakamura, A. / Tanaka, I. / Yao, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 258.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 199 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 538.9 KB | Display | |
Data in XML | ![]() | 40.2 KB | Display | |
Data in CIF | ![]() | 55.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x6cC ![]() 1b23S ![]() 3wkrS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 47538.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 2661 / Gene: MJ1678 / Production host: ![]() ![]() #2: Protein | Mass: 25334.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ1481 / Production host: ![]() ![]() #3: RNA chain | | Mass: 24129.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #4: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE ENTITY SEQUENCE OF THE CHAIN I OR J MAPPED TO GB AAB99700.1 RESIDUE 1 TO 396. | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.33 % |
---|---|
Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5 / Details: 0.1M MES pH 5.0, 2.4M Ammonium Sulfate / PH range: 5.0-5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: CCD / Date: Oct 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.596→48.221 Å / Num. obs: 59370 / % possible obs: 99.7 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 18.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3WKR, 1B23 Resolution: 2.596→48.221 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.94
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.596→48.221 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|