[English] 日本語
![](img/lk-miru.gif)
- PDB-1ym1: X-ray crystallographic structure of CTX-M-9 beta-lactamase comple... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ym1 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystallographic structure of CTX-M-9 beta-lactamase complexed with a boronic acid inhibitor (SM2) | ||||||
![]() | beta-lactamase CTX-M-9a | ||||||
![]() | HYDROLASE / CTX-M / beta-lactamase / transition state / deacylation / boronic acid | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Y. / Shoichet, B. / Bonnet, R. | ||||||
![]() | ![]() Title: Structure, Function, and Inhibition along the Reaction Coordinate of CTX-M beta-Lactamases. Authors: Chen, Y. / Shoichet, B. / Bonnet, R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 257.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 207.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 992.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 996.8 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 48.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ylyC ![]() 1ylzC ![]() 1ymsC ![]() 1ymxC ![]() 1yljS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 27972.494 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.69 Å3/Da / Density % sol: 27.4 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 8.8 Details: potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2004 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→30 Å / Num. obs: 143714 / % possible obs: 85.1 % / Observed criterion σ(I): -3 / Redundancy: 9.01 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.12→1.16 Å / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 1.92 / % possible all: 23.1 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1YLJ Resolution: 1.12→10 Å / Num. parameters: 46244 / Num. restraintsaints: 58327 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT. RIDING HYDROGENS INCLUDED IN REFINEMENT. THIS STRUCTURE CONTAINS BOTH APO AND COMPLEX STATES IN EACH MONOMER.
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 86 / Occupancy sum hydrogen: 3767.81 / Occupancy sum non hydrogen: 4732.8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|