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- PDB-6com: 2.3A crystal structure of E. coli phosphoenolpyruvate carboxykina... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6com | |||||||||
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Title | 2.3A crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Asp269Asn | |||||||||
![]() | Phosphoenolpyruvate carboxykinase (ATP) | |||||||||
![]() | LYASE / enzyme / Pepcarboxykinase | |||||||||
Function / homology | ![]() phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / calcium ion binding / magnesium ion binding / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sokaribo, A.S. / Cotelesage, J.H. / Novakovski, B. / Goldie, H. / Sanders, D. | |||||||||
![]() | ![]() Title: Kinetic and structural analysis of Escherichia coli phosphoenolpyruvate carboxykinase mutants. Authors: Sokaribo, A. / Novakovski, B.A.A. / Cotelesage, J. / White, A.P. / Sanders, D. / Goldie, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.8 KB | Display | ![]() |
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PDB format | ![]() | 93.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v2lC ![]() 6v2mC ![]() 6v2nC ![]() 1aylS 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59708.191 Da / Num. of mol.: 1 / Mutation: D269N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP) |
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-Non-polymers , 5 types, 304 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ATP / |
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#3: Chemical | ChemComp-PYR / |
#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8.2 Details: A 2ul drop with 2 mg/ml protein, 5 mM Calcium chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate, 0.01 mM DTT, 30% PEG 4000 ...Details: A 2ul drop with 2 mg/ml protein, 5 mM Calcium chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate, 0.01 mM DTT, 30% PEG 4000 was added to 2 ul drop containing 2 M sodium aceate, 0.1 M Tris pH 8.2 30% PEG 4000. After a week a rod like crystal was removed and soaked in a solution with 30% glycerol 1mM EDTA, 100 mM sodium acetate 200mM ammonium acetate and 12% PEG 4000. The crystal was put into a loop and flash cooled in liquid notrogen |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→50 Å / Num. obs: 77150 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.98 Å2 / Rmerge(I) obs: 0.25 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.11→2.19 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AYL Resolution: 2.3→47.087 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.67 Å2 / Biso mean: 24.5497 Å2 / Biso min: 10.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→47.087 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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