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Open data
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Basic information
Entry | Database: PDB / ID: 8edt | |||||||||
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Title | E. coli Pyruvate kinase (PykF) T462I | |||||||||
![]() | Pyruvate kinase![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Donovan, K.A. / Coombes, D. / Dobson, R.C.J. / Cooper, T.F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Beneficial mutations occurring in E. coli pyruvate kinase afford new allosteric mechanisms leading to faster resumption of growth Authors: Donovan, K.A. / Coombes, D. / Dobson, R.C.J. / Cooper, T.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 333.3 KB | Display | ![]() |
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PDB format | ![]() | 273.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8edqC ![]() 8edrC ![]() 8edsC ![]() 8eq0C ![]() 8eq1C ![]() 8eq3C ![]() 8eu4C ![]() 4yngS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 50804.379 Da / Num. of mol.: 2 / Mutation: T462I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.36 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M (0.2M 1,6-Hexanediol; 0.2M 1-Butanol 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1M (Imidazole; MES monohydrate (acid)), 30% v/v (40% v/v ...Details: 0.1 M (0.2M 1,6-Hexanediol; 0.2M 1-Butanol 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1M (Imidazole; MES monohydrate (acid)), 30% v/v (40% v/v Ethylene glycol; 20 % w/v PEG 8000), 100uM 1,8-ANS |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.09→40.89 Å / Num. obs: 71661 / % possible obs: 99.96 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.69 |
Reflection shell | Resolution: 2.09→2.165 Å / Rmerge(I) obs: 0.7768 / Num. unique obs: 7046 / CC1/2: 0.335 / % possible all: 99.97 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4YNG Resolution: 2.09→40.89 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 23.12 / Stereochemistry target values: MLHL
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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 max: 147.51 Å2 / Biso mean: 45.5312 Å2 / Biso min: 11.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→40.89 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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