+Open data
-Basic information
Entry | Database: PDB / ID: 5b62 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of N-terminal amidase with Asn-Glu-Ala peptide | ||||||
Components |
| ||||||
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 / : / Nta1p Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae CEN.PK113-7D (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.042 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5b62.cif.gz | 100 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5b62.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 5b62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/5b62 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/5b62 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5hyyC 5k5uC 5k5vC 5k60C 5k61C 5k62C 5k63C 5k66C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 52049.840 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 |
---|---|
#2: Protein/peptide | Mass: 332.310 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Saccharomyces cerevisiae CEN.PK113-7D (yeast) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.57 % |
---|---|
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 |
---|---|
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: 3.04→33.041 Å / Num. obs: 10652 / % possible obs: 99.9 % / Redundancy: 13.2 % / Net I/σ(I): 32.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.042→33.041 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.67
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.042→33.041 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|