+Open data
-Basic information
Entry | Database: PDB / ID: 1urb | ||||||
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Title | ALKALINE PHOSPHATASE (N51MG) | ||||||
Components | ALKALINE PHOSPHATASE | ||||||
Keywords | ALKALINE PHOSPHATASE / HYDROLASE / PHOSPHORIC MONOESTER / PHOSPHO TRANSFERASE / ALCOHOL ACCEPTOR | ||||||
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: 2.14 Å | ||||||
Authors | Tibbitts, T.T. / Murphy, J.E. / Kantrowitz, E.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Kinetic and structural consequences of replacing the aspartate bridge by asparagine in the catalytic metal triad of Escherichia coli alkaline phosphatase. Authors: Tibbitts, T.T. / Murphy, J.E. / Kantrowitz, E.R. #1: Journal: J.Mol.Biol. / Year: 1995 Title: Mutations at Positions 153 and 328 in Escherichia Coli Alkaline Phosphatase Provide Insight Towards the Structure and Function of Mammalian and Yeast Alkaline Phosphatases Authors: Murphy, J.E. / Tibbitts, T.T. / Kantrowitz, E.R. #2: Journal: Protein Sci. / Year: 1994 Title: Kinetics and Crystal Structure of a Mutant E. Coli Alkaline Phosphatase (Asp-369->Asn): A Mechanism Involving One Zinc Per Active Site Authors: Tibbitts, T.T. / Xu, X. / Kantrowitz, E.R. #3: 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 | 1urb.cif.gz | 179.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1urb.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 1urb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/1urb ftp://data.pdbj.org/pub/pdb/validation_reports/ur/1urb | 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 | THERE IS A DIMER (IDENTICAL CHAINS OF 449 RESIDUES) PER ASYMMETRIC UNIT. THESE SUBUNITS ARE DESIGNATED "A" AND "B". |
-Components
#1: Protein | Mass: 46766.074 Da / Num. of mol.: 2 / Mutation: D51N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EK1734 / Gene: PHOA / Plasmid: PEK247 / Gene (production host): PHOA / Production host: Escherichia coli (E. coli) / Strain (production host): SM547 / References: UniProt: P00634, alkaline phosphatase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Compound details | THE STRUCTURE IS OF A MUTANT ALKALINE PHOSPHATE (D51N) IN WHICH ASP-51 IS REPLACED BY ASN. THERE ...THE STRUCTURE IS OF A MUTANT ALKALINE PHOSPHATE (D51N) IN WHICH ASP-51 IS REPLACED BY ASN. THERE ARE TWO ZINCS COMPLEXED WITH AN INORGANIC PHOSPHATE BOUND IN EACH OF THE TWO ACTIVE SITES. THE THIRD METAL BIN SITE IS UNOCCUPIED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.42 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9.2 Details: 45% SATURATING (NH4)2SO4, 0.10 MM CAPS, 20 MM MGCL2, 10 UM ZNCL2, 0.1 MM NAH2PO4 AT PH 9.2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9.5 / Method: vapor diffusion, hanging drop / Details: Chen, L. C., (1992) Protein Eng., 5, 605. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Date: Sep 28, 1994 |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 61905 / % possible obs: 88.3 % / Observed criterion σ(I): 3 |
Reflection | *PLUS Highest resolution: 2.14 Å / Redundancy: 3 % / Num. measured all: 186425 / Rmerge(I) obs: 0.086 |
-Processing
Software |
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Refinement | Resolution: 2.14→8 Å / σ(F): 2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→8 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS
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