[English] 日本語
![](img/lk-miru.gif)
- PDB-1qxw: Crystal structure of Staphyloccocus aureus in complex with an ami... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1qxw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Staphyloccocus aureus in complex with an aminoketone inhibitor 54135. | ||||||
![]() | methionyl aminopeptidase | ||||||
![]() | HYDROLASE / pita bread fold | ||||||
Function / homology | ![]() initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / transition metal ion binding / proteolysis Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Douangamath, A. / Dale, G.E. / D'Arcy, A. / Oefner, C. | ||||||
![]() | ![]() Title: Crystal structures of staphylococcusaureus methionine aminopeptidase complexed with keto heterocycle and aminoketone inhibitors reveal the formation of a tetrahedral intermediate. Authors: Douangamath, A. / Dale, G.E. / D'Arcy, A. / Almstetter, M. / Eckl, R. / Frutos-Hoener, A. / Henkel, B. / Illgen, K. / Nerdinger, S. / Schulz, H. / MacSweeney, A. / Thormann, M. / Treml, A. / ...Authors: Douangamath, A. / Dale, G.E. / D'Arcy, A. / Almstetter, M. / Eckl, R. / Frutos-Hoener, A. / Henkel, B. / Illgen, K. / Nerdinger, S. / Schulz, H. / MacSweeney, A. / Thormann, M. / Treml, A. / Pierau, S. / Wadman, S. / Oefner, C. | ||||||
History |
| ||||||
Remark 600 | heterogen The original inhibitor used in the crystal was 3-Amino-1-cyclopropylamino-heptan-2-one. ...heterogen The original inhibitor used in the crystal was 3-Amino-1-cyclopropylamino-heptan-2-one. The M1C coordinates in this structure are those of a transition state complex of the inhibitor. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 71.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 449.6 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 27535.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A080, UniProt: P0A078*PLUS, methionyl aminopeptidase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-M1C / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.09 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 294 K / Method: microbatch / pH: 5.5 Details: PEG 3350, Bis-tris, ammonium acetate, pH 5.5, microbatch, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: batch method / Details: Oefner, C., (2003) J. Mol. Biol., 332, 13. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 2002 |
Radiation | Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.57 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→20 Å / Num. all: 29574 / Num. obs: 29278 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 14 Å2 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.67→1.77 Å / Mean I/σ(I) obs: 8.6 / % possible all: 96.7 |
Reflection | *PLUS Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS % possible obs: 96.7 % / Rmerge(I) obs: 0.117 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.793 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.67→1.76 Å / Total num. of bins used: 10 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.185 / Rfactor Rwork: 0.158 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|