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Yorodumi- PDB-1ed9: STRUCTURE OF E. COLI ALKALINE PHOSPHATASE WITHOUT THE INORGANIC P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ed9 | ||||||
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Title | STRUCTURE OF E. COLI ALKALINE PHOSPHATASE WITHOUT THE INORGANIC PHOSPHATE AT 1.75A RESOLUTION | ||||||
Components | ALKALINE PHOSPHATASE | ||||||
Keywords | HYDROLASE / wild type / free of phosphate | ||||||
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 / Resolution: 1.75 Å | ||||||
Authors | Stec, B. / Holtz, K.M. / Kantrowitz, E.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: A revised mechanism for the alkaline phosphatase reaction involving three metal ions. Authors: Stec, B. / Holtz, K.M. / Kantrowitz, E.R. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two-metal ion catalysis. Authors: Kim, E.E. / Wyckoff, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ed9.cif.gz | 190.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ed9.ent.gz | 157.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ed9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/1ed9 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/1ed9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47094.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PEK48 / Production host: Escherichia coli (E. coli) / 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: 3.3 Å3/Da / Density % sol: 62.77 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Tris, ammonium sulfate, magnesium chloride, zinc chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: UCSD MARK II / Detector: AREA DETECTOR / Date: Mar 31, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→35 Å / Num. all: 116126 / Num. obs: 116126 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.0637 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.75→1.88 Å / Redundancy: 1.76 % / Rmerge(I) obs: 0.328 / Num. unique all: 18331 / % possible all: 73.4 |
Reflection | *PLUS Redundancy: 3.3 % |
Reflection shell | *PLUS % possible obs: 75.1 % / Mean I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Resolution: 1.75→15 Å / Num. parameters: 29907 / Num. restraintsaints: 28661 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Conjugate gradient refinement. Last cycle with full matrix.
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Solvent computation | Solvent model: moews & kretsinger | |||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 6386 / Occupancy sum non hydrogen: 7234.78 | |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→15 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4 % / Rfactor all: 0.196 / Rfactor obs: 0.164 / Rfactor Rfree: 0.236 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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