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- PDB-7ds7: The Crystal Structure of Leaf-branch compost cutinase from Biortus. -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ds7 | ||||||
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Title | The Crystal Structure of Leaf-branch compost cutinase from Biortus. | ||||||
![]() | Leaf-branch compost cutinase | ||||||
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Function / homology | ![]() poly(ethylene terephthalate) hydrolase / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wang, F. / Lv, Z. / Cheng, W. / Lin, D. / Chu, F. / Xu, X. / Tan, J. | ||||||
![]() | ![]() Title: The Crystal Structure of Leaf-branch compost cutinase from Biortus. Authors: Wang, F. / Lv, Z. / Cheng, W. / Lin, D. / Chu, F. / Xu, X. / Tan, 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 | ![]() | 68.6 KB | Display | ![]() |
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PDB format | ![]() | 45.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6thtS S: Starting model for refinement |
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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: 29805.250 Da / Num. of mol.: 1 / Mutation: Y127G,S165A,D238C,F243I,S283C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() ![]() References: UniProt: G9BY57, ![]() |
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#2: Chemical | ChemComp-IMD / ![]() |
#3: Chemical | ChemComp-GOL / ![]() |
#4: Chemical | ChemComp-CIT / ![]() |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.62 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.6M imidazole, 0.1M tri-sodium citrate PH7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→47.38 Å / Num. obs: 13146 / % possible obs: 98.1 % / Redundancy: 11 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.15→2.22 Å / Rmerge(I) obs: 0.262 / Num. unique obs: 1117 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6tht Resolution: 2.15→47.38 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.606 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.286 / ESU R Free: 0.206 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.937 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→47.38 Å
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Refine LS restraints |
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LS refinement shell |
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