[English] 日本語
![](img/lk-miru.gif)
- PDB-2hb9: Crystal Structure of the Zinc-Beta-Lactamase L1 from Stenotrophom... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2hb9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Zinc-Beta-Lactamase L1 from Stenotrophomonas Maltophilia (Inhibitor 3) | ||||||
![]() | Metallo-beta-lactamase L1 | ||||||
![]() | HYDROLASE / METALLO / ZN / LACTAMASE | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nauton, L. / Garau, G. / Kahn, R. / Dideberg, O. | ||||||
![]() | ![]() Title: Structural insights into the design of inhibitors for the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia. Authors: Nauton, L. / Kahn, R. / Garau, G. / Hernandez, J.F. / Dideberg, O. #1: ![]() Title: Update of the Standard Numbering Scheme for Class B Beta-Lactamases Authors: Garau, G. / Garcia-Saez, I. / Bebrone, C. / Anne, C. / Mercuri, P. / Galleni, M. / Frere, J.-M. / Dideberg, O. #2: ![]() Title: The 3-D Structure of a Zinc Metallo-Beta-Lactamase from Bacillus Cereus Reveals a New Type of Protein Fold Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.-M. / Dideberg, O. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE RESIDUE NUMBERING OF THE COORDINATES IS NON-SEQUENTIAL. MANY NUMBERS WERE SIMPLY ... SEQUENCE THE RESIDUE NUMBERING OF THE COORDINATES IS NON-SEQUENTIAL. MANY NUMBERS WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 71.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 457.3 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fm6C ![]() 2fu7C ![]() 2fu8C ![]() 2fu9C ![]() 2gfjC ![]() 2gfkC ![]() 2h6aC ![]() 1smlS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 28740.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: IID 1275 / Cellular location: PERIPLASM / Gene: L1 / Plasmid: PET26 / Production host: ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: 1.8M AMMONIUM SULFATE, 0.1M HEPES PH 7.75, 1.5% V/V PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→19.51 Å / Num. all: 31993 / Num. obs: 31993 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.059 / Rsym value: 0.054 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2 / Rsym value: 0.287 / % possible all: 99.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SML Resolution: 1.75→19.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.747 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.876 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→19.67 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
|