+Open data
-Basic information
Entry | Database: PDB / ID: 1ely | ||||||
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Title | E. COLI ALKALINE PHOSPHATASE MUTANT (S102C) | ||||||
Components | ALKALINE PHOSPHATASE | ||||||
Keywords | HYDROLASE / ALKALINE PHOSPHATASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Stec, B. / Hehir, M. / Brennan, C. / Nolte, M. / Kantrowitz, E.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Kinetic and X-ray structural studies of three mutant E. coli alkaline phosphatases: insights into the catalytic mechanism without the nucleophile Ser102. Authors: Stec, B. / Hehir, M.J. / Brennan, C. / Nolte, 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 | 1ely.cif.gz | 176.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ely.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 1ely.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/1ely ftp://data.pdbj.org/pub/pdb/validation_reports/el/1ely | HTTPS FTP |
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-Related structure data
Related structure data | 1elxC 1elzC 1alkS 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.007209, 0.999972, -0.002197), Vector: |
-Components
#1: Protein | Mass: 47110.461 Da / Num. of mol.: 2 / Mutation: S102C Source method: isolated from a genetically manipulated source Details: ENZYME INHIBITED WITH PHOSPHATE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: SM547 / Gene: PHOA / Plasmid: PEK306 / 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: 56.81 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 25 MG/ML PROTEIN IN 39% SATURATING (NH4)2SO4, 100 MM TRIS, 10 MM MGCL2 100 MM ZNCL2, 2 MM NAH2PO4 AT PH 7.5, EQUILIBRATED AGAINST 55% SATURATING (NH4)2SO4 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Aug 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48 Å / Num. obs: 25172 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 1 / % possible all: 84.7 |
Reflection shell | *PLUS % possible obs: 84.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ALK Resolution: 2.8→9 Å / Isotropic thermal model: ALL ATOMS / Cross valid method: IMPLOR-CYCLING TEST SETS / σ(F): 2
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Displacement parameters | Biso mean: 13.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.64 Å / Total num. of bins used: 20
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.194 |