+Open data
-Basic information
Entry | Database: PDB / ID: 5hyy | ||||||
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Title | Crystal structure of N-terminal amidase | ||||||
Components | Nta1p | ||||||
Keywords | HYDROLASE / N-end rule / Nitrilase superfamily / Nta1 | ||||||
Function / homology | Protein N-terminal amidase / protein-N-terminal glutamine amidohydrolase activity / protein-N-terminal asparagine amidohydrolase activity / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / protein catabolic process / Nta1p Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.323 Å | ||||||
Authors | Kim, M.K. / Lee, B.-G. / Oh, S.-J. / 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 | 5hyy.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hyy.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 5hyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/5hyy ftp://data.pdbj.org/pub/pdb/validation_reports/hy/5hyy | HTTPS FTP |
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-Related structure data
Related structure data | 5b62C 5k5uC 5k5vC 5k60C 5k61C 5k62C 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: 52065.906 Da / Num. of mol.: 1 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: 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: 2.65 Å3/Da / Density % sol: 53.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M Ammonium acetate, 0.1M TriNa citrate dihydrate pH5.6, 30%(w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2012 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→37.509 Å / Num. obs: 23487 / % possible obs: 99.9 % / Redundancy: 8.1 % / Net I/σ(I): 42.4 |
-Processing
Software |
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Refinement | Resolution: 2.323→37.509 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 27.34 / 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: 2.323→37.509 Å
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Refine LS restraints |
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LS refinement shell |
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