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- PDB-7tff: Crystal structure of human platelet phosphofructokinase-1 mutant-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tff | ||||||
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Title | Crystal structure of human platelet phosphofructokinase-1 mutant- D564N | ||||||
![]() | ATP-dependent 6-phosphofructokinase, platelet type | ||||||
![]() | TRANSFERASE / Kinase / Somatic mutation | ||||||
Function / homology | ![]() 6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / cellular response to leukemia inhibitory factor / cadherin binding ...6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / cellular response to leukemia inhibitory factor / cadherin binding / protein-containing complex binding / extracellular exosome / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hansen, H. / Webb, B.A. / Robart, A.R. / Narayanasami, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cancer-associated somatic mutations in human phosphofructokinase-1 reveal a critical electrostatic interaction for allosteric regulation of enzyme activity. Authors: Voronkova, M.A. / Hansen, H.L. / Cooper, M.P. / Miller, J. / Sukumar, N. / Geldenhuys, W.J. / Robart, A.R. / Webb, B.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 | ![]() | 691.5 KB | Display | ![]() |
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PDB format | ![]() | 459.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502 KB | Display | ![]() |
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Full document | ![]() | 534.1 KB | Display | |
Data in XML | ![]() | 98.4 KB | Display | |
Data in CIF | ![]() | 130.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xykS S: Starting model for refinement |
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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: 89143.742 Da / Num. of mol.: 4 / Mutation: D564N Source method: isolated from a genetically manipulated source Details: recombinant PFKP with His tag, mutation D564N / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.75 % |
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Crystal grow | Temperature: 295.15 K / Method: microbatch / pH: 5.5 Details: 125uM ATP, 25% PEG3350, 0.2M ammonium sulfate, 0.1M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→161.74 Å / Num. obs: 36675 / % possible obs: 98.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 127.22 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.132 / Rrim(I) all: 0.25 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 3.6→3.76 Å / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4395 / Rpim(I) all: 0.742 / Rrim(I) all: 1.377 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4XYK Resolution: 3.6→66.57 Å / SU ML: 0.6923 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4338 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: 117.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→66.57 Å
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Refine LS restraints |
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LS refinement shell |
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