[English] 日本語
![](img/lk-miru.gif)
- PDB-2pqc: CP4 EPSPS liganded with (R)-phosphonate tetrahedral reaction inte... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2pqc | ||||||
---|---|---|---|---|---|---|---|
Title | CP4 EPSPS liganded with (R)-phosphonate tetrahedral reaction intermediate analog | ||||||
![]() | 3-phosphoshikimate 1-carboxyvinyltransferase | ||||||
![]() | TRANSFERASE / inside-out alpha/beta barrel | ||||||
Function / homology | ![]() 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase activity / response to herbicide / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Healy-Fried, M.L. / Funke, T. / Han, H. / Schonbrunn, E. | ||||||
![]() | ![]() Title: Differential inhibition of class I and class II 5-enolpyruvylshikimate-3-phosphate synthases by tetrahedral reaction intermediate analogues. Authors: Funke, T. / Healy-Fried, M.L. / Han, H. / Alberg, D.G. / Bartlett, P.A. / Schonbrunn, E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 106.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 79.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 878.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 880.8 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pq9C ![]() 2pqbC ![]() 2pqdC ![]() 2ggaS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 46665.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9R4E4, 3-phosphoshikimate 1-carboxyvinyltransferase |
---|---|
#2: Chemical | ChemComp-RC1 / [ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.38 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: (NH4)2SO4, KCl, PEG 400, HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 14, 2007 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→15 Å / Num. all: 54614 / Num. obs: 54614 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 3 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 7.2 / Num. unique all: 4686 / % possible all: 97.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 2GGA Resolution: 1.6→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 69.482 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.167 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→15 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|