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Yorodumi- PDB-1p48: REVERSE PROTONATION IS THE KEY TO GENERAL ACID-BASE CATALYSIS IN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p48 | ||||||
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Title | REVERSE PROTONATION IS THE KEY TO GENERAL ACID-BASE CATALYSIS IN ENOLASE | ||||||
Components | Enolase 1 | ||||||
Keywords | LYASE / BETA BARREL | ||||||
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 | Sims, P.A. / Larsen, T.M. / Poyner, R.R. / Cleland, W.W. / Reed, G.H. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Reverse protonation is the key to general acid-base catalysis in enolase Authors: Sims, P.A. / Larsen, T.M. / Poyner, R.R. / Cleland, W.W. / Reed, G.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p48.cif.gz | 191.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p48.ent.gz | 148.9 KB | Display | PDB format |
PDBx/mmJSON format | 1p48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p48_validation.pdf.gz | 387.2 KB | Display | wwPDB validaton report |
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Full document | 1p48_full_validation.pdf.gz | 396.1 KB | Display | |
Data in XML | 1p48_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1p48_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/1p48 ftp://data.pdbj.org/pub/pdb/validation_reports/p4/1p48 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer. There is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 46731.812 Da / Num. of mol.: 2 / Mutation: E211Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ENO1 OR ENOA OR HSP48 OR YGR254W OR G9160 / Production host: Escherichia coli (E. coli) / References: UniProt: P00924, phosphopyruvate hydratase #2: Chemical | ChemComp-MG / #3: Chemical | #4: 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: 2.41 Å3/Da / Density % sol: 49.02 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: batch / pH: 8 Details: PEG 8000, potassium chloride, HEPPS, pH 8.0, Batch, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: BRUKER PROTEUM R / Detector: CCD / Date: Oct 23, 2001 / Details: Montel Optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 61265 / Num. obs: 61265 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.064 |
Reflection shell | Resolution: 2→2.09 Å / Rsym value: 0.189 / % possible all: 99 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / % possible obs: 99 % / Num. measured all: 231529 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.189 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS |