+Open data
-Basic information
Entry | Database: PDB / ID: 7wg2 | ||||||
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Title | EVAA-KlAte1 | ||||||
Components | Arginyltransferase | ||||||
Keywords | TRANSFERASE / Arginyl-tRNA protein transferase 1 | ||||||
Function / homology | arginyltransferase / arginyl-tRNA--protein transferase activity / N-end aminoacyl transferase, N-terminal / N-end rule aminoacyl transferase, C-terminal / N-end rule aminoacyl transferase / Arginine-tRNA-protein transferase, N terminus / Arginine-tRNA-protein transferase, C terminus / Acyl-CoA N-acyltransferase / Arginyl-tRNA--protein transferase 1 Function and homology information | ||||||
Biological species | Kluyveromyces lactis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å | ||||||
Authors | Kim, M.K. / Kim, B.H. / Oh, S.-J. / Song, H.K. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates. Authors: Kim, B.H. / Kim, M.K. / Oh, S.J. / Nguyen, K.T. / Kim, J.H. / Varshavsky, A. / Hwang, C.S. / Song, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wg2.cif.gz | 364.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wg2.ent.gz | 250.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/7wg2 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/7wg2 | HTTPS FTP |
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-Related structure data
Related structure data | 7wfxC 7wg1C 7wg4C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57942.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Gene: KLLA0_A04862g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CXX6, arginyltransferase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 60mM Divalents (Molecular dimensions), 100mM buffer system 2 pH 7.5 (Molecular dimensions), 33% (v/v) precipitant Mix 4 (Molecular dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→29.49 Å / Num. obs: 61443 / % possible obs: 99.93 % / Redundancy: 26.5 % / Biso Wilson estimate: 25.87 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.99 |
Reflection shell | Resolution: 1.76→1.823 Å / Num. unique obs: 6037 / CC1/2: 0.711 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.76→29.49 Å / SU ML: 0.2186 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5507 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→29.49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 26.3073367442 Å / Origin y: -6.84595739382 Å / Origin z: 13.2674168783 Å
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Refinement TLS group | Selection details: all |