[English] 日本語
Yorodumi- PDB-1tem: 6 ALPHA HYDROXYMETHYL PENICILLOIC ACID ACYLATED ON THE TEM-1 BETA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tem | ||||||
---|---|---|---|---|---|---|---|
Title | 6 ALPHA HYDROXYMETHYL PENICILLOIC ACID ACYLATED ON THE TEM-1 BETA-LACTAMASE FROM ESCHERICHIA COLI | ||||||
Components | TEM-1 BETA LACTAMASE | ||||||
Keywords | HYDROLASE / ANTIBIOTIC RESISTANCE / TRANSPOSABLE ELEMENT | ||||||
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 / Resolution: 1.95 Å | ||||||
Authors | Maveyraud, L. / Massova, I. / Samama, J.P. / Mobashery, S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1996 Title: Crystal Structure of 6Alpha-Hydroxymethylpenicillanate Complexed to the Tem-1 Beta-Lactamase from Escherichia Coli: Evidence on the Mechanism of Action of a Novel Inhibitor Designed by a Computer-Aided Process Authors: Maveyraud, L. / Massova, I. / Birck, C. / Miyashita, K. / Samama, J.P. / Mobashery, S. #1: Journal: J.Am.Chem.Soc. / Year: 1995 Title: Design, Synthesis, and Evaluation of a Potent Mechanism-Based Inhibitor for the Tem Beta-Lactamase with Implications for the Enzyme Mechanism Authors: Miyashita, K. / Massova, I. / Taibi, P. / Mobashery, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1tem.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1tem.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tem_validation.pdf.gz | 376.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1tem_full_validation.pdf.gz | 377.7 KB | Display | |
Data in XML | 1tem_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1tem_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/1tem ftp://data.pdbj.org/pub/pdb/validation_reports/te/1tem | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28984.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: VARIANT V84I, A184V,ACYL-ENZYME COMPLEX / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase |
---|---|
#2: Chemical | ChemComp-ALP / |
#3: Water | ChemComp-HOH / |
Compound details | THE STRUCTURE DEPOSITED IS AN ACYL-ENZYME COMPLEX, BETWEEN 6ALPHA-HYDROXYMETHYL PENICILLOIC ACID ...THE STRUCTURE DEPOSITED IS AN ACYL-ENZYME COMPLEX, BETWEEN 6ALPHA-HYDROXYMET |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.52 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.8 / Details: pH 7.8 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 6 ℃ / Method: vapor diffusion, hanging drop / Details: Jelsch, C., (1992) J. Mol. Biol., 223, 377. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 263 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 0.933 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Num. obs: 17104 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 12.49 Å2 / Rmerge(I) obs: 0.046 |
Reflection | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 22 Å / Num. measured all: 42284 |
Reflection shell | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 2.02 Å / % possible obs: 94.8 % / Num. unique obs: 1524 / Num. measured obs: 3622 / Rmerge(I) obs: 0.076 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.95→8 Å / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→1.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 12.359 Å2 |