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Yorodumi- PDB-2one: ASYMMETRIC YEAST ENOLASE DIMER COMPLEXED WITH RESOLVED 2'-PHOSPHO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2one | ||||||
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Title | ASYMMETRIC YEAST ENOLASE DIMER COMPLEXED WITH RESOLVED 2'-PHOSPHOGLYCERATE 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lebioda, L. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Mechanism of enolase: the crystal structure of asymmetric dimer enolase-2-phospho-D-glycerate/enolase-phosphoenolpyruvate at 2.0 A resolution. Authors: Zhang, E. / Brewer, J.M. / Minor, W. / Carreira, L.A. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2one.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2one.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 2one.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2one_validation.pdf.gz | 413.4 KB | Display | wwPDB validaton report |
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Full document | 2one_full_validation.pdf.gz | 479.6 KB | Display | |
Data in XML | 2one_validation.xml.gz | 28 KB | Display | |
Data in CIF | 2one_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/2one ftp://data.pdbj.org/pub/pdb/validation_reports/on/2one | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 361 molecules
#2: Chemical | #3: Chemical | ChemComp-LI / | #4: Chemical | ChemComp-2PG / | #5: Chemical | ChemComp-PEP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 / Details: pH 7.8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→9 Å / Num. obs: 29854 / % possible obs: 83.3 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.056 |
Reflection | *PLUS Num. measured all: 96445 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: YEAST ENOLASE Resolution: 2→9 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→9 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.137 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_deg / Dev ideal: 3.1 |