+Open data
-Basic information
Entry | Database: PDB / ID: 1b8j | ||||||
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Title | ALKALINE PHOSPHATASE COMPLEXED WITH VANADATE | ||||||
Components | PROTEIN (ALKALINE PHOSPHATASE) | ||||||
Keywords | ALKALINE PHOSPHATASE / HYDROLASE / PHOSPHORIC MONOESTER / TRANSFERASE (PHOSPHO / ALCOHOL ACCEPTOR) / VANADATE | ||||||
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: 1.9 Å | ||||||
Authors | Holtz, K.M. / Stec, B. / Kantrowitz, E.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: A model of the transition state in the alkaline phosphatase reaction. Authors: Holtz, K.M. / Stec, B. / Kantrowitz, E.R. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Trapping and Visualization of a Covalent Enzyme-Phosphate Intermediate Authors: Murphy, J.E. / Stec, B. / Ma, L. / Kantrowitz, E.R. #2: 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 | 1b8j.cif.gz | 199.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b8j.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 1b8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b8j ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b8j | HTTPS FTP |
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-Related structure data
Related structure data | 1alkS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.908718, 0.117698, -0.400474), Vector: |
-Components
#1: Protein | Mass: 47209.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: VANADATE COVALENTLY BOUND TO SERINE NUCLEOPHILE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: SM547 / Cellular location: PERIPLASM / Gene: PHOA / Plasmid: PEK154 / Cellular location (production host): PERIPLASM / Gene (production host): PHOA / Production host: Escherichia coli (E. coli) / Strain (production host): SM547 / 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: 62.96 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: CRYSTALLIZATION CONDITIONS: 65 % SATURATING (NH4)2SO4, 100 MM TRIS, 10 MM MGCL2, 1 MM ZNCL2, 0.1 MM NH4VO3, PH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
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: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: May 1, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→26.42 Å / Num. obs: 93722 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 26.46 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.9→2.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 0.92 / % possible all: 85.3 |
Reflection | *PLUS Num. measured all: 266977 |
Reflection shell | *PLUS % possible obs: 85.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ALK Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 19.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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