+Open data
-Basic information
Entry | Database: PDB / ID: 5k62 | ||||||
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Title | Crystal structure of N-terminal amidase C187S | ||||||
Components | Nta1p | ||||||
Keywords | HYDROLASE / N-end rule / Nitrilase superfamily / Nta1 | ||||||
Function / homology | Function and homology information protein-N-terminal glutamine amidohydrolase activity / protein-N-terminal asparagine amidohydrolase activity / protein catabolic process Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.899 Å | ||||||
Authors | Kim, M.K. / Oh, S.-J. / Lee, B.-G. / Song, H.K. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway. Authors: Kim, M.K. / Oh, S.J. / Lee, B.G. / 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 | 5k62.cif.gz | 108.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k62.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 5k62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/5k62 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/5k62 | HTTPS FTP |
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-Related structure data
Related structure data | 5b62C 5hyyC 5k5uC 5k5vC 5k60C 5k61C 5k63C 5k66C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 52049.840 Da / Num. of mol.: 1 / Mutation: C187S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain CEN.PK113-7D) (yeast) Strain: CEN.PK113-7D / Gene: CENPK1137D_1355 / Production host: Escherichia coli (E. coli) / References: UniProt: N1P8Q8 |
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#2: Chemical | ChemComp-ASN / |
#3: Chemical | ChemComp-VAL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Mg acetate tetrahydrate, 0.2M Na cacodylate pH6.5, 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Oct 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.899→29.307 Å / Num. obs: 43119 / % possible obs: 99.6 % / Redundancy: 16.2 % / Net I/σ(I): 72.6 |
-Processing
Software |
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Refinement | Resolution: 1.899→29.307 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.899→29.307 Å
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Refine LS restraints |
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LS refinement shell |
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