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Open data
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Basic information
Entry | Database: PDB / ID: 5hyy | ||||||
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Title | Crystal structure of N-terminal amidase | ||||||
![]() | Nta1p | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kim, M.K. / Lee, B.-G. / Oh, S.-J. / Song, H.K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98 KB | Display | ![]() |
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PDB format | ![]() | 73.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.8 KB | Display | ![]() |
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Full document | ![]() | 431.2 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b62C ![]() 5k5uC ![]() 5k5vC ![]() 5k60C ![]() 5k61C ![]() 5k62C ![]() 5k63C ![]() 5k66C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Strain: CEN.PK113-7D / Gene: CENPK1137D_1355 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() |
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 |
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Processing
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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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