[English] 日本語
![](img/lk-miru.gif)
- PDB-2qmw: The crystal structure of the prephenate dehydratase (PDT) from St... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2qmw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The crystal structure of the prephenate dehydratase (PDT) from Staphylococcus aureus subsp. aureus Mu50 | |||||||||
![]() | Prephenate dehydratase | |||||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC85812 / prephenate dehydratase (PDT) / Staphylococcus aureus subsp. aureus Mu50 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | |||||||||
Function / homology | ![]() prephenate dehydratase / prephenate dehydratase activity / L-phenylalanine biosynthetic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tan, K. / Zhang, R. / Li, H. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
![]() | ![]() Title: Structures of open (R) and close (T) states of prephenate dehydratase (PDT) - implication of allosteric regulation by L-phenylalanine. Authors: Tan, K. / Li, H. / Zhang, R. / Gu, M. / Clancy, S.T. / Joachimiak, A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 111.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 92.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 498.7 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The Chain A forms a dimer with its symmetry-related molecule (1-x,1-y,z). Similarly, the Chain B forms a dimer with its symmetry-related molecule (1-x,1-y,z). The two dimers form a tetramer. |
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30002.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Species: Staphylococcus aureus / Strain: Mu50 / Gene: SAV1915 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 102 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-ACT / | ||||
#4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.47 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M Sodium citrate, 3M Sodium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2006 / Details: mirror | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.3→45.88 Å / Num. all: 25930 / Num. obs: 25930 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 56.5 | |||||||||
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1672 / % possible all: 97.8 |
-
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: 63.484 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→45.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.355 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|