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- PDB-3vwr: Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vwr | |||||||||
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Title | Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/R187G/H266N/D370Y mutant complexd with 6-aminohexanoate | |||||||||
![]() | 6-aminohexanoate-dimer hydrolase![]() | |||||||||
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Function / homology | ![]() 6-aminohexanoate-oligomer exohydrolase / ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kawashima, Y. / Shibata, N. / Negoro, S. / Higuchi, Y. | |||||||||
![]() | ![]() Title: Structural, kinetic and theoretical analyses of hydrolase mutants altering in the directionality and equilibrium point of reversible amide-synthetic/hydrolytic reaction Authors: Negoro, S. / Kawashima, Y. / Shibata, N. / Shigeta, Y. / Kobayashi, T. / Nishiguchi, H. / Matsui, T. / Baba, T. / Lee, Y. / Kamiya, K. / Kato, D. / Takeo, M. / Higuchi, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.9 KB | Display | ![]() |
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PDB format | ![]() | 73.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 42805.434 Da / Num. of mol.: 1 / Mutation: S112A, G181D, R187G, H266N, D370Y Source method: isolated from a genetically manipulated source Details: THE FUSION PROTEIN OF RESIDUES 1-21 FROM NYLON OLIGOMERS-DEGRADING ENZYME EII (UNP P07061) AND RESIDUES 22-392 FROM NYLON OLIGOMERS-DEGRADING ENZYME EII' (UNP Q59710) Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P07061, UniProt: Q59710, UniProt: P07062*PLUS, 6-aminohexanoate-oligomer exohydrolase |
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-Non-polymers , 5 types, 391 molecules ![](data/chem/img/ACA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACA / ![]() | ||||||
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#3: Chemical | ChemComp-GOL / ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-SO4 / | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.19 % / Mosaicity: 0.3 ° |
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Crystal grow![]() | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.2M AMMONIUM SULFATE, 0.2M LITHIUM SULFATE, 0.1M MES, pH 6.5, vapor diffusion, sitting drop, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 26, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→30.38 Å / Num. obs: 80141 / % possible obs: 99.1 % / Redundancy: 4.82 % / Rmerge(I) obs: 0.032 / Χ2: 0.79 / Net I/σ(I): 21.8 / Scaling rejects: 2923 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.6151 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.8 Å2 / Biso mean: 21.9393 Å2 / Biso min: 6.44 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→29.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.71 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
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Xplor file |
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