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- PDB-2zm2: Structure of 6-aminohexanoate-dimer hydrolase, A61V/A124V/R187S/F... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zm2 | ||||||
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Title | Structure of 6-aminohexanoate-dimer hydrolase, A61V/A124V/R187S/F264C/G291R/G338A/D370Y mutant (Hyb-S4M94) | ||||||
![]() | 6-aminohexanoate-dimer hydrolase | ||||||
![]() | HYDROLASE / ALPHA-BETA | ||||||
Function / homology | ![]() 6-aminohexanoate-oligomer exohydrolase / 6-aminohexanoate-dimer hydrolase activity / nylon catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ohki, T. / Shibata, N. / Higuchi, Y. / Kawashima, Y. / Takeo, M. / Kato, D. / Nego, S. | ||||||
![]() | ![]() Title: Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase. Authors: Ohki, T. / Shibata, N. / Higuchi, Y. / Kawashima, Y. / Takeo, M. / Kato, D. / Negoro, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.3 KB | Display | ![]() |
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PDB format | ![]() | 76.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.8 KB | Display | ![]() |
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Full document | ![]() | 473 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zlyC ![]() 2zm8C ![]() 2zm9C ![]() 1wybS C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 42943.711 Da / Num. of mol.: 1 / Mutation: A61V, A124V, R187S, F264C, G291R, G338A, D370Y Source method: isolated from a genetically manipulated source Details: CHIMERA OF NYLON OLIGOMERS-DEGRADING ENZYME EII (RESIDUES 1-21) AND NYLON OLIGOMERS-DEGRADING ENZYME EII' (RESIDUES 22-392) Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P07061, UniProt: P07062, 6-aminohexanoate-oligomer exohydrolase | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MES / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | ACCORDING TO DEPOSITORS | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.33 % |
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Crystal grow | Temperature: 283 K / pH: 6.5 Details: 2.2M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, pH 6.50, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 96878 / Num. obs: 96878 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 44.91 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.26 / Num. unique all: 8782 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WYB Resolution: 1.55→33.64 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1845983.03 / 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: 62.0769 Å2 / ksol: 0.387215 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→33.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.61 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
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