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- PDB-6wup: Crystal structure of an ancestral cyclohexadienyl dehydratase, An... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wup | |||||||||
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Title | Crystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-5 | |||||||||
![]() | Ancestral cyclohexadienyl dehydratase, AncCDT-5 | |||||||||
![]() | LYASE / cyclohexadienyl dehydratase ancestral protein reconstruction | |||||||||
Function / homology | Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kaczmarski, J.A. / Mahawaththa, M.C. | |||||||||
![]() | ![]() Title: Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme. Authors: Kaczmarski, J.A. / Mahawaththa, M.C. / Feintuch, A. / Clifton, B.E. / Adams, L.A. / Goldfarb, D. / Otting, G. / Jackson, C.J. #1: ![]() Title: Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein. Authors: Clifton, B. / Kaczmarski, J.A. / Carr, P.D. / Gerth, M.L. / Tokuriki, N. / Jackson, C.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 | ![]() | 77.4 KB | Display | ![]() |
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PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.3 KB | Display | ![]() |
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Full document | ![]() | 435.1 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oki 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26966.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-EPE / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20 % w/v PEG 6000, 0.2 M MgCl2, 0.1 M HEPES, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→43.85 Å / Num. obs: 43661 / % possible obs: 100 % / Redundancy: 35.3 % / Biso Wilson estimate: 25.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.019 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.49→1.52 Å / Redundancy: 30.3 % / Rmerge(I) obs: 3.9 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2105 / CC1/2: 0.501 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6OKI ![]() 6oki Resolution: 1.49→35.69 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4522 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→35.69 Å
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Refine LS restraints |
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LS refinement shell |
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