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Yorodumi- PDB-1y7a: Structure of D153H/K328W E. coli alkaline phosphatase in presence... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y7a | ||||||
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Title | Structure of D153H/K328W E. coli alkaline phosphatase in presence of cobalt at 1.77 A resolution | ||||||
Components | Alkaline phosphatase | ||||||
Keywords | HYDROLASE / metal specificity / high-spin/low-spin configurations | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Wang, J. / Stieglitz, K. / Kantrowitz, E.R. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Metal Specificity Is Correlated with Two Crucial Active Site Residues in Escherichia coli Alkaline Phosphatase(,). Authors: Wang, J. / Stieglitz, K.A. / 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 | 1y7a.cif.gz | 191.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y7a.ent.gz | 150.2 KB | Display | PDB format |
PDBx/mmJSON format | 1y7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/1y7a ftp://data.pdbj.org/pub/pdb/validation_reports/y7/1y7a | HTTPS FTP |
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-Related structure data
Related structure data | 1y6vC 1ed8S 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
#1: Protein | Mass: 47174.488 Da / Num. of mol.: 2 / Mutation: D153H, K328W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: phoA / Plasmid: pEK548 / Production host: Escherichia coli (E. coli) / Strain (production host): SM547 / References: UniProt: P00634, alkaline phosphatase #2: Chemical | ChemComp-CO / #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: 57.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 10 mM cobalt chloride, 2.2 M ammonium sulfate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2003 / Details: Monochromatic |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.77→30 Å / Num. obs: 117928 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.239 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ED8 Resolution: 1.77→30 Å / Cross valid method: THOUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.77→30 Å
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