+Open data
-Basic information
Entry | Database: PDB / ID: 8edr | |||||||||
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Title | E. coli pyruvate kinase (PykF) P70Q | |||||||||
Components | Pyruvate kinase | |||||||||
Keywords | TRANSFERASE / Pyruvate kinase / Long term evolution experiment / Kinase | |||||||||
Function / homology | Function and homology information pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / phosphorylation / magnesium ion binding / ATP binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | |||||||||
Authors | Donovan, K.A. / Coombes, D. / Dobson, R.C.J. / Cooper, T.F. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8edr.cif.gz | 333.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8edr.ent.gz | 273.6 KB | Display | PDB format |
PDBx/mmJSON format | 8edr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/8edr ftp://data.pdbj.org/pub/pdb/validation_reports/ed/8edr | HTTPS FTP |
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-Related structure data
Related structure data | 8edqC 8edsC 8edtC 8eq0C 8eq1C 8eq3C 8eu4C 4yngS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50823.340 Da / Num. of mol.: 2 / Mutation: P70Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pykF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2TL68, pyruvate kinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.12M (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1M (1.0M Imidazole; MES monohydrate (acid)), 30% v/v (40% v/v Ethylene glycol; 20 % w/v PEG 8000) |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→41.83 Å / Num. obs: 33761 / % possible obs: 94.8 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.03724 / Net I/σ(I): 19.78 |
Reflection shell | Resolution: 2.64→2.734 Å / Rmerge(I) obs: 0.3222 / Mean I/σ(I) obs: 2.42 / Num. unique obs: 2381 / CC1/2: 0.796 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YNG Resolution: 2.64→41.83 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.57 / Stereochemistry target values: ML
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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: 168.68 Å2 / Biso mean: 37.1334 Å2 / Biso min: 10.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.64→41.83 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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