[English] 日本語
Yorodumi- PDB-1khj: E. COLI ALKALINE PHOSPHATASE MUTANT (D153HD330N) MIMIC OF THE TRA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1khj | ||||||
---|---|---|---|---|---|---|---|
Title | E. COLI ALKALINE PHOSPHATASE MUTANT (D153HD330N) 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: 2.3 Å | ||||||
Authors | Le Du, M.H. / Lamoure, C. / Muller, B.H. / Bulgakov, O.V. / Lajeunesse, E. / Menez, A. / Boulain, J.C. | ||||||
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 | 1khj.cif.gz | 183.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1khj.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 1khj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/1khj ftp://data.pdbj.org/pub/pdb/validation_reports/kh/1khj | HTTPS FTP |
---|
-Related structure data
Related structure data | 1kh4SC 1kh5C 1kh7C 1kh9C 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: 47115.484 Da / Num. of mol.: 2 / Mutation: D153H, 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 | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.46 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 292 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 / Wavelength: 1.5418 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 | |||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.3→20 Å / Num. all: 49163 / Num. obs: 49163 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Rsym value: 0.011 | |||||||||
Reflection shell | Resolution: 2.3→2.44 Å / Rsym value: 0.48 / % possible all: 95 | |||||||||
Reflection | *PLUS Rmerge(I) obs: 0.11 | |||||||||
Reflection shell | *PLUS Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1KH4 Resolution: 2.3→10 Å / Cross valid method: IMPLOR-CYCLING TEST SETS / σ(F): 0 / Stereochemistry target values: XPLOR
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.3 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.257 / Rfactor obs: 0.257 |