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Open data
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Basic information
Entry | Database: PDB / ID: 3o8o | ||||||
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Title | Structure of phosphofructokinase from Saccharomyces cerevisiae | ||||||
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![]() | TRANSFERASE / kinase | ||||||
Function / homology | ![]() 6-phosphofructokinase complex / vacuolar proton-transporting V-type ATPase complex assembly / 6-phosphofructokinase / Glycolysis / 6-phosphofructokinase activity / fructose-6-phosphate binding / glucose catabolic process / fructose 6-phosphate metabolic process / canonical glycolysis / monosaccharide binding ...6-phosphofructokinase complex / vacuolar proton-transporting V-type ATPase complex assembly / 6-phosphofructokinase / Glycolysis / 6-phosphofructokinase activity / fructose-6-phosphate binding / glucose catabolic process / fructose 6-phosphate metabolic process / canonical glycolysis / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / vacuolar acidification / AMP binding / proton transmembrane transport / Neutrophil degranulation / glycolytic process / regulation of intracellular pH / protein homotetramerization / mitochondrial outer membrane / mRNA binding / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Banaszak, K. / Mechin, I. / Kopperschlager, G. / Rypniewski, W. | ||||||
![]() | ![]() Title: The Crystal Structures of Eukaryotic Phosphofructokinases from Baker's Yeast and Rabbit Skeletal Muscle. Authors: Banaszak, K. / Mechin, I. / Obmolova, G. / Oldham, M. / Chang, S.H. / Ruiz, T. / Radermacher, M. / Kopperschlager, G. / Rypniewski, W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 911.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.3 MB | Display | ![]() |
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Full document | ![]() | 4.6 MB | Display | |
Data in XML | ![]() | 232 KB | Display | |
Data in CIF | ![]() | 306.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3o8lC ![]() 3o8nC ![]() 1pfkS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 86002.547 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PFK1, YGR240C, G8599 / Production host: ![]() ![]() #2: Protein | Mass: 83537.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PFK2, YMR205C, YM8325.06C / Production host: ![]() ![]() #3: Sugar | ChemComp-F6P / #4: Sugar | ChemComp-FDP / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.92 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 6-10% PEG4000, 0.2 mM sodium acetate, 0.1 M MES buffer pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 28, 1997 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1044 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→35 Å / Num. all: 172818 / Num. obs: 172818 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.075 / Net I/σ(I): 15.13 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.75 / Rsym value: 0.557 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PFK Resolution: 2.9→35 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→35 Å
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Refine LS restraints |
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Xplor file |
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