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- PDB-3bdf: Crystal structure of metal-free E. coli alkaline phosphatase (T155V) -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bdf | ||||||
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Title | Crystal structure of metal-free E. coli alkaline phosphatase (T155V) | ||||||
![]() | Alkaline phosphatase | ||||||
![]() | HYDROLASE / bacterial alkaline phosphatase / Magnesium / Metal-binding / Periplasm / Phosphorylation / Zinc | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Grigg, J.C. / Murphy, M.E. | ||||||
![]() | ![]() Title: The Active-Site Trimetallic Cluster of Alkaline Phosphatase is Lost Upon Isosteric Mutation at the Mg2+-Coordinating Residue Threonine-155 Authors: Grigg, J.C. / Hucaluk, C. / Murphy, M.E. / Ritter, H. / Yee, J. / Rafferty, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.2 KB | Display | ![]() |
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PDB format | ![]() | 158 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.3 KB | Display | ![]() |
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Full document | ![]() | 455.6 KB | Display | |
Data in XML | ![]() | 43.6 KB | Display | |
Data in CIF | ![]() | 69 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bdgC ![]() 3bdhC ![]() 1ed9S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48320.758 Da / Num. of mol.: 2 / Mutation: T155V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES, 0.2 M LiSO4, 1 mM ZnCl2, 5 mM MgCl2, 25-30% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2007 Details: Vertical focusing mirror, single crystal (Si111) bent monochromator (horizontal focusing) |
Radiation | Monochromator: side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 210186 / Redundancy: 3.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1ED9 Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.839 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.036 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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