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Yorodumi- PDB-2ga3: Structure of S102T E. coli Alkaline Phosphatase-phosphate interme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ga3 | ||||||
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Title | Structure of S102T E. coli Alkaline Phosphatase-phosphate intermediate at 2.20A resolution | ||||||
Components | Alkaline phosphatase | ||||||
Keywords | HYDROLASE / mutagenesis / side chain conformation / covalent intermediate / rate-determining step | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / dephosphorylation / protein dephosphorylation / outer membrane-bounded periplasmic space / periplasmic space / magnesium ion binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wang, J. / Kantrowitz, E.R. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Trapping the tetrahedral intermediate in the alkaline phosphatase reaction by substitution of the active site serine with threonine. Authors: Wang, J. / Kantrowitz, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ga3.cif.gz | 186.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ga3.ent.gz | 146.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ga3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/2ga3 ftp://data.pdbj.org/pub/pdb/validation_reports/ga/2ga3 | HTTPS FTP |
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-Related structure data
Related structure data | 2g9yC 1y6vS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit contains the biologically active dimer |
-Components
#1: Protein | Mass: 47188.402 Da / Num. of mol.: 2 / Mutation: S102(TPO) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: phoA / Plasmid: pEK625 / Production host: Escherichia coli (E. coli) / Strain (production host): SM547 / References: UniProt: P00634, alkaline phosphatase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: 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: 3.21 Å3/Da / Density % sol: 61.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 2.0M ammonium sulfate, 100mM Tris, 10mM magnesium chloride, 0.01mM zinc chloride, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 26, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→14.98 Å / Num. all: 61826 / Num. obs: 55150 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.47 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.352 / Num. unique all: 6110 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1Y6V Resolution: 2.2→14.98 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→14.98 Å
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Refine LS restraints |
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