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Yorodumi- PDB-1kh9: E. COLI ALKALINE PHOSPHATASE MUTANT (D153GD330N) COMPLEX WITH PHO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kh9 | ||||||
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Title | E. COLI ALKALINE PHOSPHATASE MUTANT (D153GD330N) COMPLEX WITH PHOSPHATE | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Le Du, M.H. / Lamoure, C. / Muller, B.H. / Bulgakov, O.V. / Lajeunesse, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Artificial evolution of an enzyme active site: structural studies of three highly active mutants of Escherichia coli alkaline phosphatase. Authors: Le Du, M.H. / Lamoure, C. / Muller, B.H. / Bulgakov, O.V. / Lajeunesse, E. / Menez, A. / Boulain, J.C. #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 | 1kh9.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kh9.ent.gz | 139.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/1kh9 ftp://data.pdbj.org/pub/pdb/validation_reports/kh/1kh9 | HTTPS FTP |
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-Related structure data
Related structure data | 1kh4C 1kh5C 1kh7SC 1khjC 1khkC 1khlC 1khnC 1i23 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.00713, 0.999974, -0.001354), Vector: |
-Components
#1: Protein | Mass: 47092.426 Da / Num. of mol.: 2 / Mutation: D153G, D330N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: WCC118 / Plasmid: PLIP4.0D153HD330N / Production host: Escherichia coli (E. coli) / References: UniProt: P00634, alkaline phosphatase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / | #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: 2.86 Å3/Da / Density % sol: 57.01 % |
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Crystal grow | Temperature: 292 K / pH: 8 Details: ammonium sulfate, magnesium chloride, zinc sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1 |
Detector | Type: SDMS / Date: Jul 1, 1996 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 32077 / % possible obs: 83.4 % / Observed criterion σ(I): 0 / Rsym value: 0.118 |
Reflection shell | Resolution: 2.5→2.64 Å / Rsym value: 0.698 / % possible all: 80.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1KH7 Resolution: 2.5→10 Å / Cross valid method: IMPLOR-CYCLING TEST SETS / σ(F): 2 / Stereochemistry target values: XPLOR
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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LS refinement shell | Resolution: 2.5→2.64 Å / Total num. of bins used: 20
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