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Yorodumi- PDB-3a65: Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a65 | |||||||||
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Title | Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/H266N mutant with substrate | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Kawashima, Y. / Shibata, N. / Higuchi, Y. / Takeo, M. / Negoro, S. | |||||||||
Citation | Journal: To be Published Title: Enzymatic Synthesis of Nylon-6 Units in Organic Sol Contained Low-Water: Structural Requirement of 6-Aminohexanoate-Dimer Hydrolase for Efficient Amid Synthesis Authors: Kawashima, Y. / Yasuhira, K. / Shibata, N. / Matsuura, Y. / Tanaka, Y. / Taniguchi, M. / Miyoshi, Y. / Takeo, M. / Kato, D. / Higuchi, Y. / Negoro, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a65.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a65.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 3a65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a65_validation.pdf.gz | 469.2 KB | Display | wwPDB validaton report |
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Full document | 3a65_full_validation.pdf.gz | 473.5 KB | Display | |
Data in XML | 3a65_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 3a65_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/3a65 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/3a65 | HTTPS FTP |
-Related structure data
Related structure data | 3a66C 1wycS 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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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: 42857.488 Da / Num. of mol.: 1 / Mutation: S112A, G181D, H266N 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.) Flavobacterium (bacteria) / Strain: K172 Description: Strain of the source organism is described KI72 in the first reference of the d atabase UniProtKB/Swiss-Prot P07061 (NYLB_FLASK) and P07062 (NYLC_FLASK). Gene: nylB, NYLB' / Plasmid: PKP1500 / Production host: Escherichia coli (E. coli) / Strain (production host): KP3998 References: UniProt: P07061, UniProt: P07062, 6-aminohexanoate-oligomer exohydrolase |
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-Non-polymers , 5 types, 493 molecules
#2: Chemical | ChemComp-ACA / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | ACCORDING TO DEPOSITORS |
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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: 3.53 Å3/Da / Density % sol: 65.19 % |
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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 6.50, 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 |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 7, 2008 |
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→31.56 Å / Num. obs: 65321 / % possible obs: 96.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 10 / Redundancy: 3.33 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.038 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.2 / % possible all: 76.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WYC Resolution: 1.7→31.56 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 729414.73 / 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: 63.2391 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→31.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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