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- PDB-6kuo: Crystal strcuture of PETase N246D mutant from Ideonella sakaiensis -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kuo | ||||||
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Title | Crystal strcuture of PETase N246D mutant from Ideonella sakaiensis | ||||||
![]() | Poly(ethylene terephthalate) hydrolase | ||||||
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Function / homology | ![]() poly(ethylene terephthalate) hydrolase / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joo, S. / Kim, K.-J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 44 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kuqC ![]() 6kusC ![]() 5xjhS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31491.900 Da / Num. of mol.: 1 / Mutation: N246D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ISF6_4831 / Production host: ![]() ![]() ![]() References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.63 % |
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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: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→50 Å / Num. obs: 21787 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rrim(I) all: 0.077 / Net I/σ(I): 29.78 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 1072 / Rrim(I) all: 0.329 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5XJH Resolution: 1.9→31.06 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.693 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.113 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: 76.87 Å2 / Biso mean: 22.705 Å2 / Biso min: 10.03 Å2
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Refinement step | Cycle: final / Resolution: 1.9→31.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.951 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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