[English] 日本語
![](img/lk-miru.gif)
- PDB-1rf6: Structural Studies of Streptococcus pneumoniae EPSP Synthase in S... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1rf6 | ||||||
---|---|---|---|---|---|---|---|
Title | Structural Studies of Streptococcus pneumoniae EPSP Synthase in S3P-GLP Bound State | ||||||
![]() | 5-enolpyruvylshikimate-3-phosphate synthase | ||||||
![]() | TRANSFERASE / shikimate pathway / EPSP synthase / S3P / Glyphosate / PEP / S. pneumoniae | ||||||
Function / homology | ![]() 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, H. / Hilsenbeck, J.L. / Kim, H.J. / Shuttleworth, W.A. / Park, Y.H. / Evans, J.N. / Kang, C. | ||||||
![]() | ![]() Title: Structural studies of Streptococcus pneumoniae EPSP synthase in unliganded state, tetrahedral intermediate-bound state and S3P-GLP-bound state. Authors: Park, H. / Hilsenbeck, J.L. / Kim, H.J. / Shuttleworth, W.A. / Park, Y.H. / Evans, J.N. / Kang, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 339.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 276.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 76.2 KB | Display | |
Data in CIF | ![]() | 105.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a monomer |
-
Components
#1: Protein | Mass: 45878.820 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9S400, 3-phosphoshikimate 1-carboxyvinyltransferase #2: Chemical | ChemComp-GPJ / #3: Chemical | ChemComp-S3P / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.94 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG, EG, NaCl, Na/K phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 188141 / Num. obs: 188141 / % possible obs: 94.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.9→2 Å / % possible all: 92.8 |
Reflection | *PLUS Num. measured all: 982621 / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 92.8 % / Rmerge(I) obs: 0.065 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.264 / Rfactor Rwork: 0.205 |