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Yorodumi- PDB-1alk: REACTION MECHANISM OF ALKALINE PHOSPHATASE BASED ON CRYSTAL STRUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1alk | ||||||
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Title | REACTION MECHANISM OF ALKALINE PHOSPHATASE BASED ON CRYSTAL STRUCTURES. TWO METAL ION CATALYSIS | ||||||
Components | ALKALINE PHOSPHATASE | ||||||
Keywords | 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 / Resolution: 2 Å | ||||||
Authors | Kim, E.E. / Wyckoff, W. | ||||||
Citation | 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. #1: Journal: J.Biol.Chem. / Year: 1991 Title: Bacillus Subtilis Alkaline Phosphatases III and Iv. Cloning, Sequencing, and Comparisons of Deduced Amino Acid Sequence with Escherichia Coli Alkaline Phosphatase Three-Dimensional Structure Authors: Hulett, F.M. / Kim, E.E. / Bookstein, C. / Kapp, N.V. / Edwards, C.W. / Wyckoff, H.W. #2: Journal: Clin.Chim.Acta / Year: 1989 Title: Structure of Alkaline Phosphatases Authors: Kim, E.E. / Wyckoff, H.W. #3: Journal: J.Mol.Biol. / Year: 1985 Title: Refined Structure of Alkaline Phosphatase Authors: Sowadski, J.M. / Handschumacher, M.D. / Murthy, H.M.K. / Foster, B.A. / 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 | 1alk.cif.gz | 166.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1alk.ent.gz | 138.8 KB | Display | PDB format |
PDBx/mmJSON format | 1alk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/1alk ftp://data.pdbj.org/pub/pdb/validation_reports/al/1alk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES 1-4 AND 404-409 ARE NOT WELL DEFINED IN THE ELECTRON DENSITY MAPS. | ||||||||
Details | THERE IS A DIMER (IDENTICAL CHAIN OF 449 RESIDUES) PER ASYMMETRIC UNIT AND THEY ARE REFINED INDEPENDENTLY. |
-Components
#1: Protein | Mass: 47093.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00634, alkaline phosphatase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THERE ARE THREE WATER MOLECULES COORDINATING TO THE THIRD METAL, NAMELY MG (RESIDUE NUMBER 452 ), ...THERE ARE THREE WATER MOLECULES COORDINATI | Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.02 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 9.5 / Method: microdialysis | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 17164 / Rmerge(I) obs: 0.047 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.177 / Rfactor obs: 0.177 / Highest resolution: 2 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 5 Å / Rfactor obs: 0.177 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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