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- PDB-6q7r: Crystal structure of OE1.3 alkylated with the mechanistic inhibit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6q7r | |||||||||
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Title | Crystal structure of OE1.3 alkylated with the mechanistic inhibitor 2-bromoacetophenone | |||||||||
![]() | OE1.3 | |||||||||
![]() | HYDROLASE / Computationally designed enzyme | |||||||||
Function / homology | ![]() N-acylneuraminate-9-phosphatase activity / N-acetylneuraminate biosynthetic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Levy, C.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Design and evolution of an enzyme with a non-canonical organocatalytic mechanism. Authors: Burke, A.J. / Lovelock, S.L. / Frese, A. / Crawshaw, R. / Ortmayer, M. / Dunstan, M. / Levy, C. / Green, A.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.4 KB | Display | ![]() |
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PDB format | ![]() | 136.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6q7nC ![]() 6q7oC ![]() 6q7pC ![]() 6q7qC ![]() 2uw6S 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: 27607.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-AC0 / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-PEG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.02 M calcium chloride dihydrate 0.1 M sodium acetate pH 4.6, 30 % v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40.74 Å / Num. obs: 43399 / % possible obs: 99.95 % / Redundancy: 6.4 % / Biso Wilson estimate: 17.03 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Net I/σ(I): 16.63 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.74 / Num. unique obs: 4256 / CC1/2: 0.874 / Rpim(I) all: 0.2283 / Rrim(I) all: 0.5846 / % possible all: 99.91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2UW6 Resolution: 1.5→40.74 Å / SU ML: 0.1273 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.7946
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→40.74 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.980239176 Å / Origin y: 11.8693971559 Å / Origin z: -12.5935679048 Å
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Refinement TLS group | Selection details: all |