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Yorodumi- PDB-1ew9: ALKALINE PHOSPHATASE (E.C. 3.1.3.1) COMPLEX WITH MERCAPTOMETHYL P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ew9 | ||||||
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Title | ALKALINE PHOSPHATASE (E.C. 3.1.3.1) COMPLEX WITH MERCAPTOMETHYL PHOSPHONATE | ||||||
Components | ALKALINE PHOSPHATASE | ||||||
Keywords | HYDROLASE / enzyme-inhibitor complex | ||||||
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: 2 Å | ||||||
Authors | Holtz, K.M. / Stec, B. / Meyers, J.K. / Antonelli, S.M. / Widlanski, T.S. / Kantrowitz, E.R. | ||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: Alternate modes of binding in two crystal structures of alkaline phosphatase-inhibitor complexes. Authors: Holtz, K.M. / Stec, B. / Myers, J.K. / Antonelli, S.M. / Widlanski, T.S. / Kantrowitz, E.R. #1: Journal: J.Biol.Chem. / Year: 1999 Title: A Model of the Transition State in the Alkaline Phosphatase Reaction Authors: Holtz, K.M. / Stec, B. / Kantrowitz, E.R. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Reaction Mechanism of Alkaline Phosphatase Based on Two 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 | 1ew9.cif.gz | 189.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ew9.ent.gz | 149.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ew9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/1ew9 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/1ew9 | 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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Details | homodimeric metalloenzyme with a non-crystallographic 2-fold symmetry axis |
-Components
-Protein , 1 types, 2 molecules AB
#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) / Strain: SM547 / Cellular location: PERIPLASM / Gene: PHOA / Plasmid: PEK154 / Production host: Escherichia coli (E. coli) / References: UniProt: P00634, alkaline phosphatase |
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-Non-polymers , 5 types, 569 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | The magnesium 452 has three waters associated with it and it has been labelled as ligand MO3 for ...The magnesium 452 has three waters associated with it and it has been labelled as ligand MO3 for each chain. The zinc ion 452 has the same three waters associated with it and is labelled ZO3. The ZO3 and MO3 occupy the same space and have the same coordinates, but their occupancies are different. The MO3 is labelled as residue 452, conformation A. The ZO3 is labelled as residue 453, conformation B. SO4 558 is ASSOCIATED |
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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: 3.31 Å3/Da / Density % sol: 62.85 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: enzyme: 30 mg/mL; buffer: 40% saturated ammonium sulfate, 100 mM Tris/10 mM magnesium sulfate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: UCSD MARK III / Detector: AREA DETECTOR / Date: Aug 26, 1996 |
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: 84601 / Num. obs: 78354 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.257 / Num. unique all: 12128 / % possible all: 72.6 |
Reflection | *PLUS Num. measured all: 202714 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 72.6 % / Mean I/σ(I) obs: 1.3 |
-Processing
Software |
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Refinement | Resolution: 2→12 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Used conjugated gradient least squares for the refinement and weighted full matrix least squares procedure for estimating ESDs.
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Refinement step | Cycle: LAST / Resolution: 2→12 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.175 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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