[English] 日本語
Yorodumi- PDB-1one: YEAST ENOLASE COMPLEXED WITH AN EQUILIBRIUM MIXTURE OF 2'-PHOSPHO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1one | ||||||
---|---|---|---|---|---|---|---|
Title | YEAST ENOLASE COMPLEXED WITH AN EQUILIBRIUM MIXTURE OF 2'-PHOSPHOGLYCEATE AND PHOSPHOENOLPYRUVATE | ||||||
Components | ENOLASE | ||||||
Keywords | LYASE / GLYCOLYSIS | ||||||
Function / homology | Function and homology information Gluconeogenesis / regulation of vacuole fusion, non-autophagic / Glycolysis / melatonin binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type vacuole / glycolytic process / magnesium ion binding ...Gluconeogenesis / regulation of vacuole fusion, non-autophagic / Glycolysis / melatonin binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type vacuole / glycolytic process / magnesium ion binding / mitochondrion / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Larsen, T.M. / Wedekind, J.E. / Rayment, I. / Reed, G.H. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and ...Title: A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution. Authors: Larsen, T.M. / Wedekind, J.E. / Rayment, I. / Reed, G.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1one.cif.gz | 199.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1one.ent.gz | 155 KB | Display | PDB format |
PDBx/mmJSON format | 1one.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1one_validation.pdf.gz | 408.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1one_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 1one_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1one_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/1one ftp://data.pdbj.org/pub/pdb/validation_reports/on/1one | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 46732.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00924, phosphopyruvate hydratase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: batch method / Details: macroseeding | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 71494 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 6 Å / % possible obs: 92 % / Num. measured all: 113340 / Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / % possible obs: 81 % / Num. possible: 6132 / Rmerge(I) obs: 0.132 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→60 Å / σ(F): 0
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→60 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.177 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.009 |