+Open data
-Basic information
Entry | Database: PDB / ID: 3o8o | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of phosphofructokinase from Saccharomyces cerevisiae | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / kinase | ||||||
Function / homology | Function and homology information 6-phosphofructokinase complex / vacuolar proton-transporting V-type ATPase complex assembly / 6-phosphofructokinase / fructose-6-phosphate binding / 6-phosphofructokinase activity / Glycolysis / glucose catabolic process / vacuolar acidification / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process ...6-phosphofructokinase complex / vacuolar proton-transporting V-type ATPase complex assembly / 6-phosphofructokinase / fructose-6-phosphate binding / 6-phosphofructokinase activity / Glycolysis / glucose catabolic process / vacuolar acidification / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / AMP binding / Neutrophil degranulation / proton transmembrane transport / regulation of intracellular pH / glycolytic process / protein homotetramerization / mitochondrial outer membrane / mRNA binding / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Banaszak, K. / Mechin, I. / Kopperschlager, G. / Rypniewski, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3o8o.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3o8o.ent.gz | 911.6 KB | Display | PDB format |
PDBx/mmJSON format | 3o8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/3o8o ftp://data.pdbj.org/pub/pdb/validation_reports/o8/3o8o | HTTPS FTP |
---|
-Related structure data
Related structure data | 3o8lC 3o8nC 1pfkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 86002.547 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PFK1, YGR240C, G8599 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): PS1 / References: UniProt: P16861, 6-phosphofructokinase #2: Protein | Mass: 83537.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PFK2, YMR205C, YM8325.06C / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): PS1 / References: UniProt: P16862, 6-phosphofructokinase #3: Sugar | ChemComp-F6P / #4: Sugar | ChemComp-FDP / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.92 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1044 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|