+Open data
-Basic information
Entry | Database: PDB / ID: 7wfx | ||||||
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Title | EVAA-KlAte1 | ||||||
Components | Arginyltransferase | ||||||
Keywords | TRANSFERASE / Arginyl-tRNA protein transferase 1 | ||||||
Function / homology | Function and homology information arginyltransferase / arginyl-tRNA--protein transferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Kluyveromyces lactis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 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 | 7wfx.cif.gz | 599.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wfx.ent.gz | 502.7 KB | Display | PDB format |
PDBx/mmJSON format | 7wfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wfx_validation.pdf.gz | 671.7 KB | Display | wwPDB validaton report |
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Full document | 7wfx_full_validation.pdf.gz | 682.8 KB | Display | |
Data in XML | 7wfx_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 7wfx_validation.cif.gz | 63.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/7wfx ftp://data.pdbj.org/pub/pdb/validation_reports/wf/7wfx | HTTPS FTP |
-Related structure data
Related structure data | 7wg1C 7wg2C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 57942.285 Da / Num. of mol.: 2 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 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.21 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 120mM alcohols (Molecular dimensions), 100mM buffer system 2 pH 7.5 (Molecular dimensions), 37.5% (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: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 93872 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.071 / Rrim(I) all: 0.163 / Rsym value: 0.146 / Χ2: 0.623 / Net I/σ(I): 10.848 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.444 / Num. unique obs: 4641 / CC1/2: 0.551 / CC star: 0.843 / Rpim(I) all: 0.461 / Rrim(I) all: 0.893 / Rsym value: 0.76 / Χ2: 0.46 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→46.51 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→46.51 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: 6.2888 Å / Origin y: 119.751 Å / Origin z: 169.1095 Å
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Refinement TLS group | Selection details: all |