[English] 日本語
Yorodumi- PDB-1kh5: E. COLI ALKALINE PHOSPHATASE MUTANT (D330N) MIMIC OF THE TRANSITI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kh5 | ||||||
---|---|---|---|---|---|---|---|
Title | E. COLI ALKALINE PHOSPHATASE MUTANT (D330N) MIMIC OF THE TRANSITION STATES WITH ALUMINIUM FLUORIDE | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kh5.cif.gz | 182.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kh5.ent.gz | 143.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/1kh5 ftp://data.pdbj.org/pub/pdb/validation_reports/kh/1kh5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1kh4SC 1kh7C 1kh9C 1khjC 1khkC 1khlC 1khnC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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: D330N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: WCC118 / Gene: PHOAD153HD330N / Plasmid: PLIP4.0D153HD330N / Production host: Escherichia coli (E. coli) / References: UniProt: P00634, alkaline phosphatase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 56.81 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium sulfate, magnesium chloride, zinc sulfate, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 292 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: graphite |
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: 2→20 Å / Num. all: 68830 / Num. obs: 68830 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Rsym value: 0.086 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2→2.1 Å / Rsym value: 0.321 / % possible all: 90 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1KH4 Resolution: 2→10 Å / Cross valid method: IMPLOR-CYCLING TEST SETS / σ(F): 0
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.1 Å / Total num. of bins used: 20 /
|