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- PDB-8iax: Crystal structure of Streptococcus pneumoniae pyruvate kinase in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8iax | ||||||
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Title | Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate and fructose 1,6-bisphosphate | ||||||
![]() | Pyruvate kinase | ||||||
![]() | TRANSFERASE / Pyruvate kinase / Streptococcus pneumoniae / Glycolysis | ||||||
Function / homology | ![]() pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakashima, R. / Taguchi, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Functional and structural characterization of Streptococcus pneumoniae pyruvate kinase involved in fosfomycin resistance. Authors: Taguchi, A. / Nakashima, R. / Nishino, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 829.8 KB | Display | ![]() |
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PDB format | ![]() | 675.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 164.9 KB | Display | |
Data in CIF | ![]() | 236.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iasC ![]() 8iatC ![]() 8iauC ![]() 8iavC ![]() 8iawC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 16 molecules ABCDEFGH![](data/chem/img/FBP.gif)
![](data/chem/img/FBP.gif)
#1: Protein | Mass: 56993.590 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-FBP / |
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-Non-polymers , 4 types, 2713 molecules ![](data/chem/img/PEP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PEP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-K / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 8%(w/v) PEG3350, 50mM Citric acid/Bis-Tris Propan(3.75:6.25) pH6.75, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 5mM PEP, 10mM FBP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 21, 2023 Details: Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→48.37 Å / Num. obs: 442679 / % possible obs: 99.6 % / Redundancy: 6.99 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.068 / Net I/σ(I): 14.83 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.959 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→48.37 Å
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Refine LS restraints |
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