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Yorodumi- PDB-6kuq: Crystal strcuture of PETase A248D, R280K mutant from Ideonella sa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kuq | ||||||
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Title | Crystal strcuture of PETase A248D, R280K mutant from Ideonella sakaiensis | ||||||
Components | Poly(ethylene terephthalate) hydrolase | ||||||
Keywords | HYDROLASE / PETase / PET hydrolase | ||||||
Function / homology | Function and homology information poly(ethylene terephthalate) hydrolase / acetylesterase activity / : / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Ideonella sakaiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Joo, S. / Kim, K.-J. | ||||||
Citation | Journal: To Be Published Title: Crystal strcuture of PETase A248D, R280K mutant from Ideonella sakaiensis Authors: Joo, S. / Kim, K.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kuq.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kuq.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kuq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kuq_validation.pdf.gz | 420.2 KB | Display | wwPDB validaton report |
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Full document | 6kuq_full_validation.pdf.gz | 420.2 KB | Display | |
Data in XML | 6kuq_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 6kuq_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/6kuq ftp://data.pdbj.org/pub/pdb/validation_reports/ku/6kuq | HTTPS FTP |
-Related structure data
Related structure data | 6kuoC 6kusC 5xjhS 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
#1: Protein | Mass: 31506.908 Da / Num. of mol.: 1 / Mutation: A248D, R280K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6) (bacteria) Gene: ISF6_4831 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase |
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#2: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 17% PEG 10K, 0.1M Bis-Tris, pH 5.0, 0.15M Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97834 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97834 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 21740 / % possible obs: 98.1 % / Redundancy: 9.6 % / Rrim(I) all: 0.148 / Net I/σ(I): 55.22 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 1025 / Rrim(I) all: 0.332 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5xjh Resolution: 1.91→27.89 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.237 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.119 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.34 Å2 / Biso mean: 9.899 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 1.91→27.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.957 Å / Rfactor Rfree error: 0
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