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- PDB-5y0m: Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5y0m | ||||||
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Title | Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D36A/D122G/H130Y/E263Q mutant | ||||||
![]() | Endo-type 6-aminohexanoate oligomer hydrolase | ||||||
![]() | HYDROLASE / Nylon oligomer | ||||||
Function / homology | ![]() 6-aminohexanoate-oligomer endohydrolase / nylon catabolic process / aminopeptidase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Negoro, S. / Shibata, N. / Nagai, K. / Higuchi, Y. | ||||||
![]() | ![]() Title: Structural basis of the correct subunit assembly, aggregation, and intracellular degradation of nylon hydrolase Authors: Negoro, S. / Shibata, N. / Lee, Y.H. / Takehara, I. / Kinugasa, R. / Nagai, K. / Tanaka, Y. / Kato, D.I. / Takeo, M. / Goto, Y. / Higuchi, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 299.4 KB | Display | ![]() |
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PDB format | ![]() | 242.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480 KB | Display | ![]() |
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Full document | ![]() | 498.1 KB | Display | |
Data in XML | ![]() | 35 KB | Display | |
Data in CIF | ![]() | 52.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xygC ![]() 5xyoC ![]() 5xypC ![]() 5xyqC ![]() 5xysC ![]() 5xytC ![]() 5y0lC 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
#1: Protein | Mass: 36861.234 Da / Num. of mol.: 2 / Fragment: D36A, D122G, H130Y, E263Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Sequence details | Authors state that the long gap between the residues is due to the post-translational auto-cleavage ...Authors state that the long gap between the residues is due to the post-translational auto-cleavage of the nascent polypeptide between Asn266 and Thr267. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.2-2.2 M ammonium sulphate, 0.2 M NaCl, 0.1 M HEPES buffer pH 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→100 Å / Num. obs: 318913 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 41.9 |
Reflection shell | Resolution: 1.03→1.04 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 12557 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.788 Å2
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Refinement step | Cycle: 1 / Resolution: 1.03→72.21 Å
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Refine LS restraints |
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