+Open data
-Basic information
Entry | Database: PDB / ID: 1iyq | ||||||
---|---|---|---|---|---|---|---|
Title | Toho-1 beta-Lactamase In Complex With Benzylpenicillin | ||||||
Components | Toho-1 beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase / acyl-enzyme / complex / benzylpenicillin / penicillin G | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Shimamura, T. / Ibuka, A. / Fushinobu, S. / Wakagi, T. / Ishiguro, M. / Ishii, Y. / Matsuzawa, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Acyl-intermediate Structures of the Extended-spectrum Class A beta -Lactamase, Toho-1, in Complex with Cefotaxime, Cephalothin, and Benzylpenicillin. Authors: Shimamura, T. / Ibuka, A. / Fushinobu, S. / Wakagi, T. / Ishiguro, M. / Ishii, Y. / Matsuzawa, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1iyq.cif.gz | 66 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1iyq.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 1iyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/1iyq ftp://data.pdbj.org/pub/pdb/validation_reports/iy/1iyq | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28203.936 Da / Num. of mol.: 1 / Mutation: E166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pUC119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47066, beta-lactamase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-PNM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.55 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7 / Details: Ibuka, A., (1999) J. Mol. Biol., 285, 2079. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A |
---|---|
Detector | Type: FUJI / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 26625 / % possible obs: 92.3 % / Observed criterion σ(I): 0.1 / Rmerge(I) obs: 0.128 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 70280 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40 Å / σ(F): 3
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
| ||||||||||||||||
Refine LS restraints |
| ||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 5 % | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |