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- PDB-8foq: Crystal Structure of Kemp Eliminase 1A53-core with bound transiti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8foq | |||||||||
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Title | Crystal Structure of Kemp Eliminase 1A53-core with bound transition state analogue | |||||||||
![]() | Kemp Eliminase 1A53-core | |||||||||
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Function / homology | 5-nitro-1H-benzotriazole / ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zarifi, N. / Asthana, P. / Fraser, J.S. / Chica, R.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Kemp Eliminase 1A53-core with bound transition state analogue Authors: Zarifi, N. / Asthana, P. / Fraser, J.S. / Chica, R.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.3 KB | Display | ![]() |
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PDB format | ![]() | 135.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 29928.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / ![]() |
#3: Chemical | ChemComp-3NY / |
#4: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.239927 Å3/Da / Density % sol: 45.1216 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10 mM MES, pH 6, 40% v/v PEG400, 5% w/v PEG3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→48.48 Å / Num. obs: 34679 / % possible obs: 98.4 % / Redundancy: 8.25 % / Biso Wilson estimate: 24.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.019 / Rrim(I) all: 0.058 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 1.133 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1446 / CC1/2: 0.403 / Rpim(I) all: 0.803 / % possible all: 86 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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: 33.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→48.48 Å
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Refine LS restraints |
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LS refinement shell |
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