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Yorodumi- PDB-3vwq: 6-aminohexanoate-dimer hydrolase S112A/G181D/R187A/H266N/D370Y mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vwq | |||||||||
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Title | 6-aminohexanoate-dimer hydrolase S112A/G181D/R187A/H266N/D370Y mutant complexd with 6-aminohexanoate | |||||||||
Components | 6-aminohexanoate-dimer hydrolase | |||||||||
Keywords | HYDROLASE / NYLON DEGRADATION | |||||||||
Function / homology | Function and homology information 6-aminohexanoate-oligomer exohydrolase / 6-aminohexanoate-dimer hydrolase activity / nylon catabolic process Similarity search - Function | |||||||||
Biological species | Flavobacterium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å | |||||||||
Authors | Kawashima, Y. / Shibata, N. / Negoro, S. / Higuchi, Y. | |||||||||
Citation | Journal: to be published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vwq.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vwq.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vwq_validation.pdf.gz | 472.5 KB | Display | wwPDB validaton report |
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Full document | 3vwq_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | 3vwq_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 3vwq_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/3vwq ftp://data.pdbj.org/pub/pdb/validation_reports/vw/3vwq | HTTPS FTP |
-Related structure data
-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: 42819.461 Da / Num. of mol.: 1 / Mutation: S112A, G181D, R187A, 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.) Flavobacterium (bacteria) / Strain: K172, KI723T1 / Gene: nylB, nylB' / Plasmid: PKP1500 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KP3998 References: UniProt: P07061, UniProt: Q59710, UniProt: P07062*PLUS, 6-aminohexanoate-oligomer exohydrolase | ||||
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#2: Chemical | ChemComp-ACA / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.27 % / 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 10, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→24.97 Å / Num. obs: 67128 / % possible obs: 99.5 % / Redundancy: 4.13 % / Rmerge(I) obs: 0.035 / Χ2: 0.75 / Net I/σ(I): 18.1 / Scaling rejects: 2095 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→24.97 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 585910 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.8988 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.13 Å2 / Biso mean: 22.0606 Å2 / Biso min: 6.21 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→24.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
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Xplor file |
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