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Yorodumi- PDB-2g9y: Structure of S102T E. coli alkaline phosphatase in presence of ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g9y | ||||||
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Title | Structure of S102T E. coli alkaline phosphatase in presence of phosphate at 2.00 A 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 / 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 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 | 2g9y.cif.gz | 187.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g9y.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 2g9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g9y_validation.pdf.gz | 455.2 KB | Display | wwPDB validaton report |
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Full document | 2g9y_full_validation.pdf.gz | 466.9 KB | Display | |
Data in XML | 2g9y_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 2g9y_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/2g9y ftp://data.pdbj.org/pub/pdb/validation_reports/g9/2g9y | HTTPS FTP |
-Related structure data
Related structure data | 2ga3C 1y6vS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47108.422 Da / Num. of mol.: 2 / Mutation: S102T 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 |
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-Non-polymers , 5 types, 562 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #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: 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: Dec 24, 2003 |
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→32.7 Å / Num. all: 82178 / Num. obs: 81030 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.57 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.346 / Num. unique all: 8137 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1Y6V Resolution: 2→32.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→32.7 Å
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Refine LS restraints |
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