+Open data
-Basic information
Entry | Database: PDB / ID: 2e8i | ||||||
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Title | Structure of 6-aminohexanoate-dimer hydrolase, D1 mutant | ||||||
Components | 6-aminohexanoate-dimer hydrolase | ||||||
Keywords | HYDROLASE / ALPHA-BETA | ||||||
Function / homology | Function and homology information 6-aminohexanoate-oligomer exohydrolase / 6-aminohexanoate-dimer hydrolase activity / nylon catabolic process Similarity search - Function | ||||||
Biological species | Flavobacterium sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Shibata, N. / Higuchi, Y. / Negoro, S. | ||||||
Citation | Journal: Febs J. / Year: 2009 Title: Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold. Authors: Kawashima, Y. / Ohki, T. / Shibata, N. / Higuchi, Y. / Wakitani, Y. / Matsuura, Y. / Nakata, Y. / Takeo, M. / Kato, D. / Negoro, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e8i.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e8i.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 2e8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e8i_validation.pdf.gz | 463.3 KB | Display | wwPDB validaton report |
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Full document | 2e8i_full_validation.pdf.gz | 464.6 KB | Display | |
Data in XML | 2e8i_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 2e8i_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/2e8i ftp://data.pdbj.org/pub/pdb/validation_reports/e8/2e8i | HTTPS FTP |
-Related structure data
Related structure data | 2zm0C 2zm7C 2zmaC 1wybS 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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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 42897.531 Da / Num. of mol.: 1 / Mutation: G181D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium sp. (bacteria) / Strain: K172 / Gene: nylB, nylB' / Plasmid: pKP1500 / Production host: Escherichia coli (E. coli) References: UniProt: P07061, UniProt: P07062, 6-aminohexanoate-oligomer exohydrolase | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | ACCORDING TO DEPOSITORS, ARG190 AND HIS191 ARE CORRECT AND SWISSPROT IS INCORRECT AT THESE ...ACCORDING TO DEPOSITORS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.36 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: ammonium sulfate, lithium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-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: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 107985 / Num. obs: 107985 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 25.45 |
Reflection shell | Resolution: 1.45→1.5 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.99 / Num. unique all: 10619 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WYB Resolution: 1.45→41.87 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 266854.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.3865 Å2 / ksol: 0.376691 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→41.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.5 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
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Xplor file |
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