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Yorodumi- PDB-5xyg: Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xyg | ||||||
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Title | Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72. | ||||||
Components | Endotype 6-aminohexanoat-oligomer hydrolase | ||||||
Keywords | HYDROLASE / Nylon oligomer | ||||||
Function / homology | Function and homology information 6-aminohexanoate-oligomer endohydrolase / nylon catabolic process / aminopeptidase activity Similarity search - Function | ||||||
Biological species | Arthrobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Negoro, S. / Shibata, N. / Nagai, K. / Higuchi, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xyg.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xyg.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 5xyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xyg_validation.pdf.gz | 461.5 KB | Display | wwPDB validaton report |
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Full document | 5xyg_full_validation.pdf.gz | 467.9 KB | Display | |
Data in XML | 5xyg_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 5xyg_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/5xyg ftp://data.pdbj.org/pub/pdb/validation_reports/xy/5xyg | HTTPS FTP |
-Related structure data
Related structure data | 5xyoC 5xypC 5xyqC 5xysC 5xytC 5y0lC 5y0mC 3axgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 36939.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter sp. (bacteria) / Details (production host): PBLUESCRIPT II SK(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q79F77*PLUS #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.2-2.2M ammonium sulphate, 0.2M NaCl, 0.1M HEPES buffer pH 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 86374 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.45 / Num. unique obs: 5510 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AXG Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.093 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 20.042 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→50 Å
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Refine LS restraints |
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