[English] 日本語
![](img/lk-miru.gif)
- PDB-1jgm: High Resolution Structure of the Cadmium-containing Phosphotriest... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1jgm | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | High Resolution Structure of the Cadmium-containing Phosphotriesterase from Pseudomonas diminuta | |||||||||
![]() | Phosphotriesterase | |||||||||
![]() | HYDROLASE / PTE / Cadmium | |||||||||
Function / homology | ![]() aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Benning, M.M. / Shim, H. / Raushel, F.M. / Holden, H.M. | |||||||||
![]() | ![]() Title: High resolution X-ray structures of different metal-substituted forms of phosphotriesterase from Pseudomonas diminuta. Authors: Benning, M.M. / Shim, H. / Raushel, F.M. / Holden, H.M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 159.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 129.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 433.2 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological asembly is a dimer that is described by chains A & B in the asymmetric unit |
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36375.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 776 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.7 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: batch/microseeding / pH: 9 Details: PEG-8000, sodium chloride, phenylethyl alcohol, diethyl-4-methylbenzylphosphate, CHES, pH 9, Batch/microseeding, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 9 / Method: vapor diffusion, hanging drop / Details: Benning, M.M., (1995) Biochemistry, 34, 7973. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-2 / Detector: CCD / Date: Dec 17, 1999 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.71 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 187426 / Num. obs: 187426 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.184 / % possible all: 99 |
Reflection | *PLUS Num. measured all: 1231444 |
Reflection shell | *PLUS % possible obs: 99 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor all: 0.204 / Rfactor Rwork: 0.202 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.1 |