+Open data
-Basic information
Entry | Database: PDB / ID: 2dps | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Leucyl/phenylalanyl-tRNA-protein transferase | ||||||
Components | Leucyl/phenylalanyl-tRNA--protein transferase | ||||||
Keywords | TRANSFERASE / Aminoacyl-tRNA-protein transferase | ||||||
Function / homology | Function and homology information lysine/arginine leucyltransferase / leucyl-tRNA--protein transferase activity / aminoacyltransferase activity / protein catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Suto, K. / Shimizu, Y. / Tomita, K. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog Authors: Suto, K. / Shimizu, Y. / Watanabe, K. / Ueda, T. / Fukai, S. / Nureki, O. / Tomita, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dps.cif.gz | 102.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dps.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/2dps ftp://data.pdbj.org/pub/pdb/validation_reports/dp/2dps | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28822.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A8P1, lysine/arginine leucyltransferase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.46 % |
---|---|
Crystal grow | Temperature: 297.3 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 50mM HEPES, 0.2M tri-sodium citrate, 17%(v/v) polyethyleneglycol 3550, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 297.3K |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 2.36→50 Å / Num. all: 24541 / Num. obs: 24237 / % possible obs: 98.8 % / Observed criterion σ(F): 19.5 / Observed criterion σ(I): 26.7 / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.066 | ||||||||||||||||||
Reflection shell | Resolution: 2.36→2.44 Å / Rmerge(I) obs: 0.296 / % possible all: 92.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.4→28.85 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1462581.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.4254 Å2 / ksol: 0.333803 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→28.85 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|