+Open data
-Basic information
Entry | Database: PDB / ID: 7ckh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of TMSiPheRS | ||||||
Components | Tyrosine--tRNA ligase | ||||||
Keywords | LIGASE / AMINOACYL-TRNA SYNTHETASE / P-TRIMETHYSILYL PHENYLALANINE | ||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79492679758 Å | ||||||
Authors | Sun, J.P. / Wang, J.Y. / Zhu, Z.L. / He, Q.T. / Xiao, P. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl 1 H-NMR probe. Authors: Liu, Q. / He, Q.T. / Lyu, X. / Yang, F. / Zhu, Z.L. / Xiao, P. / Yang, Z. / Zhang, F. / Yang, Z.Y. / Wang, X.Y. / Sun, P. / Wang, Q.W. / Qu, C.X. / Gong, Z. / Lin, J.Y. / Xu, Z. / Song, S.L. ...Authors: Liu, Q. / He, Q.T. / Lyu, X. / Yang, F. / Zhu, Z.L. / Xiao, P. / Yang, Z. / Zhang, F. / Yang, Z.Y. / Wang, X.Y. / Sun, P. / Wang, Q.W. / Qu, C.X. / Gong, Z. / Lin, J.Y. / Xu, Z. / Song, S.L. / Huang, S.M. / Guo, S.C. / Han, M.J. / Zhu, K.K. / Chen, X. / Kahsai, A.W. / Xiao, K.H. / Kong, W. / Li, F.H. / Ruan, K. / Li, Z.J. / Yu, X. / Niu, X.G. / Jin, C.W. / Wang, J. / Sun, J.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ckh.cif.gz | 175.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ckh.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ckh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ckh_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ckh_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 7ckh_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 7ckh_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/7ckh ftp://data.pdbj.org/pub/pdb/validation_reports/ck/7ckh | HTTPS FTP |
-Related structure data
Related structure data | 6krgC 7ckgC 4hjrS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35912.555 Da / Num. of mol.: 2 / Mutation: Y32H,I63G,L65V,H70Q,D158G,I159G,V164G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.37 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 26% PEG 1500, 100mM Hepes, 200mM L-proline |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97891 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→49.75 Å / Num. obs: 65842 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 32.7795485647 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.79→1.83 Å / Rmerge(I) obs: 0.967 / Num. unique obs: 22047 / Rpim(I) all: 0.453 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HJR Resolution: 1.79492679758→49.7463833441 Å / SU ML: 0.200212769247 / Cross valid method: FREE R-VALUE / σ(F): 1.34352506524 / Phase error: 33.3872066858 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.3186925604 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79492679758→49.7463833441 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|