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Yorodumi- PDB-7yu2: Structure of 6-aminohexanoate-oligomer hydrolase NylC, D122G/H130... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yu2 | ||||||
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Title | Structure of 6-aminohexanoate-oligomer hydrolase NylC, D122G/H130Y/T267C mutant, hydroxylamine-treated | ||||||
Components | 6-aminohexanoate-oligomer endohydrolase | ||||||
Keywords | HYDROLASE / NYLON OLIGOMER | ||||||
Function / homology | 6-aminohexanoate-oligomer endohydrolase / Peptidase S58, DmpA / Peptidase family S58 / nylon catabolic process / ArgJ-like domain superfamily / aminopeptidase activity / 6-aminohexanoate-oligomer endohydrolase Function and homology information | ||||||
Biological species | Arthrobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å | ||||||
Authors | Negoro, S. / Higuchi, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Febs J. / Year: 2023 Title: X-ray crystallographic and mutational analysis of the NylC precursor: catalytic mechanism of autocleavage and substrate hydrolysis of nylon hydrolase. Authors: Negoro, S. / Shibata, N. / Kato, D.I. / Tanaka, Y. / Yasuhira, K. / Nagai, K. / Oshima, S. / Furuno, Y. / Yokoyama, R. / Miyazaki, K. / Takeo, M. / Hengphasatporn, K. / Shigeta, Y. / Lee, Y.H. / Higuchi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yu2.cif.gz | 496.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yu2.ent.gz | 400.1 KB | Display | PDB format |
PDBx/mmJSON format | 7yu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yu2_validation.pdf.gz | 474.4 KB | Display | wwPDB validaton report |
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Full document | 7yu2_full_validation.pdf.gz | 485.4 KB | Display | |
Data in XML | 7yu2_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 7yu2_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/7yu2 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/7yu2 | HTTPS FTP |
-Related structure data
Related structure data | 7yu0C 7yu1C 3axgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36908.266 Da / Num. of mol.: 2 / Mutation: D122G, H130Y, T267C Source method: isolated from a genetically manipulated source Details: 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. Source: (gene. exp.) Arthrobacter (bacteria) / Strain: K172 / Gene: nylC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q79F77, 6-aminohexanoate-oligomer endohydrolase #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.2 Å3/Da / Density % sol: 44.04 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.4 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→50 Å / Num. obs: 194470 / % possible obs: 99.3 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.068 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.21→1.23 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 9026 / CC1/2: 0.791 / Rrim(I) all: 0.745 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AXG Resolution: 1.21→27.145 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.221 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.032 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.963 Å2
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Refinement step | Cycle: LAST / Resolution: 1.21→27.145 Å
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Refine LS restraints |
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LS refinement shell |
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