[English] 日本語
![](img/lk-miru.gif)
- PDB-4hho: Serum paraoxonase-1 by directed evolution with the H115W mutation -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4hho | ||||||
---|---|---|---|---|---|---|---|
Title | Serum paraoxonase-1 by directed evolution with the H115W mutation | ||||||
![]() | SERUM PARAOXONASE BY DIRECTED EVOLUTION | ||||||
![]() | HYDROLASE / 6-blades -propeller fold | ||||||
Function / homology | TolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta / BROMIDE ION![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moshe, B.-D. / Grzegorz, W. / Mikael, E. / Israel, S. / Joel, L.S. / Dan, S.T. | ||||||
![]() | ![]() Title: Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme. Authors: Ben-David, M. / Wieczorek, G. / Elias, M. / Silman, I. / Sussman, J.L. / Tawfik, D.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 79.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 62.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 734.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 738 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39652.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Gene: Homo sapiens, oryctolagus cuniculus, mus musculus, rattus rattus Plasmid details: FROM SHUFFLED GENES OF HOMO SAPIENS, ORYCTOLAGUS CUNICULUS, MUS MUSCULUS, AND RATTUS Plasmid: PET32 / Production host: ![]() ![]() References: arylesterase, aryldialkylphosphatase, 1,4-lactonase | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Sugar | ChemComp-LMT / | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.44 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.2M NaBr, 0.1M Bis-tris propane , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.89 Å / Num. all: 36561 / Num. obs: 36561 / % possible obs: 99.94 % / Redundancy: 9.3 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.099 / Net I/σ(I): 26.12 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.97 / Num. unique all: 3785 / Rsym value: 0.591 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.802 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.89 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
|