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- PDB-1ew8: ALKALINE PHOSPHATASE (E.C. 3.1.3.1) COMPLEX WITH PHOSPHONOACETIC ACID -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ew8 | ||||||
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Title | ALKALINE PHOSPHATASE (E.C. 3.1.3.1) COMPLEX WITH PHOSPHONOACETIC ACID | ||||||
![]() | ALKALINE PHOSPHATASE | ||||||
![]() | HYDROLASE / enzyme-inhibitor complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Holtz, K.M. / Stec, B. / Myers, J.K. / Antonelli, S.M. / Widlanski, T.S. / Kantrowitz, E.R. | ||||||
![]() | ![]() 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: ![]() Title: A Model of the Transition State in the Alkaline Phosphatase Reaction Authors: Holtz, K.M. / Stec, B. / Kantrowitz, E.R. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189 KB | Display | ![]() |
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PDB format | ![]() | 149 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.2 KB | Display | ![]() |
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Full document | ![]() | 487 KB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 58.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | homodimeric metalloenzyme with a non-crystallographic 2-fold symmetry axis |
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 531 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PAE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PAE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | The active site has mixed occupancy with some phosphonoacetic acid (PAE) and some phosphate (PO4). ...The active site has mixed occupancy with some phosphonoacetic acid (PAE) and some phosphate (PO4). The PAE and PO4 are assigned different residue numbers, 556 and 557, and alternate conformation indicators A and B, respectively. The alternate position indicator signifies that these residues occupy the same area in space. 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 with chain A, and SO4 568 is associated with chain B. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.82 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: enzyme: 30 mg/mL; buffer: 40% saturating ammonium sulfate/100 mM Tris/10 mM MgSO4, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
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: ![]() |
Detector | Type: UCSD MARK III / Detector: AREA DETECTOR / Date: Jun 5, 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: 2.2→30 Å / Num. all: 63777 / Num. obs: 59057 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.2→2.37 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.28 / Num. unique all: 11823 / % possible all: 94 |
Reflection | *PLUS Num. measured all: 180502 |
Reflection shell | *PLUS Lowest resolution: 2.4 Å / % possible obs: 79.6 % / Redundancy: 2 % / Mean I/σ(I) obs: 1.2 |
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Processing
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Refinement | Resolution: 2.2→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: 2.2→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 all: 0.19 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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