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Yorodumi- PDB-5xyo: Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xyo | ||||||
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Title | Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D122G mutant | ||||||
Components | Endo-type 6-aminohexanoate 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 | Flavobacterium sp. KI723T1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Negoro, S. / Shibata, N. / Nagai, K. / Higuchi, Y. | ||||||
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 | 5xyo.cif.gz | 254.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xyo.ent.gz | 204 KB | Display | PDB format |
PDBx/mmJSON format | 5xyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xyo_validation.pdf.gz | 456.9 KB | Display | wwPDB validaton report |
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Full document | 5xyo_full_validation.pdf.gz | 462.4 KB | Display | |
Data in XML | 5xyo_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 5xyo_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/5xyo ftp://data.pdbj.org/pub/pdb/validation_reports/xy/5xyo | HTTPS FTP |
-Related structure data
Related structure data | 5xygSC 5xypC 5xyqC 5xysC 5xytC 5y0lC 5y0mC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5
NCS ensembles :
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-Components
#1: Protein | Mass: 36881.199 Da / Num. of mol.: 2 / Mutation: D122G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium sp. KI723T1 (bacteria) / Gene: nylC / Production host: Escherichia coli (E. coli) / References: UniProt: Q57326, UniProt: Q79F77*PLUS #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.46 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 11, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. obs: 43634 / % possible obs: 97.8 % / Redundancy: 2.79 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.05 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.2 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XYG Resolution: 2→72.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.057 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.165
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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: 27.022 Å2
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Refinement step | Cycle: 1 / Resolution: 2→72.23 Å
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Refine LS restraints |
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