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Yorodumi- PDB-2zm8: Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zm8 | |||||||||
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Title | Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer | |||||||||
Components | 6-aminohexanoate-dimer hydrolase | |||||||||
Keywords | HYDROLASE / ALPHA-BETA / 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 sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Ohki, T. / Shibata, N. / Higuchi, Y. / Kawashima, Y. / Takeo, M. / Kato, D. / Negoro, S. | |||||||||
Citation | Journal: Protein Sci. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zm8.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zm8.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zm8_validation.pdf.gz | 479.2 KB | Display | wwPDB validaton report |
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Full document | 2zm8_full_validation.pdf.gz | 482.2 KB | Display | |
Data in XML | 2zm8_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 2zm8_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/2zm8 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/2zm8 | HTTPS FTP |
-Related structure data
Related structure data | 2zlyC 2zm2C 2zm9C 2dcfS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42871.578 Da / Num. of mol.: 1 / Mutation: S112A, 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.) 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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-Non-polymers , 5 types, 487 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-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: 3.54 Å3/Da / Density % sol: 65.28 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 19, 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: 1.55→50 Å / Num. all: 88641 / Num. obs: 88641 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 41.7 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.78 / Num. unique all: 88641 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DCF Resolution: 1.55→30.43 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 483859.77 / 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: 70.3054 Å2 / ksol: 0.404024 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→30.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.61 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
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