[English] 日本語
Yorodumi- PDB-5a5z: Approved Drugs Containing Thiols as Inhibitors of Metallo-beta- l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a5z | ||||||
---|---|---|---|---|---|---|---|
Title | Approved Drugs Containing Thiols as Inhibitors of Metallo-beta- lactamases: Strategy To Combat Multidrug-Resistant Bacteria | ||||||
Components | BETA-LACTAMASE NDM-1 | ||||||
Keywords | HYDROLASE / METALLO-BETA-LACTAMASE / NDM-1 / NEW DELHI METALLO- BETA-LACTAMASE 1 / TIOPRONIN | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | KLEBSIELLA PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Klingler, F.M. / Wichelhaus, T.A. / Frank, D. / Cuesta-Bernal, J. / El-Delik, J. / Mueller, H.F. / Sjuts, H. / Goettig, S. / Koenigs, A. / Pogoryelov, D. / Proschak, E. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2015 Title: Approved Drugs Containing Thiols as Inhibitors of Metallo-beta-lactamases: Strategy To Combat Multidrug-Resistant Bacteria. Authors: Klingler, F.M. / Wichelhaus, T.A. / Frank, D. / Cuesta-Bernal, J. / El-Delik, J. / Muller, H.F. / Sjuts, H. / Gottig, S. / Koenigs, A. / Pos, K.M. / Pogoryelov, D. / Proschak, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5a5z.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5a5z.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 5a5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/5a5z ftp://data.pdbj.org/pub/pdb/validation_reports/a5/5a5z | HTTPS FTP |
---|
-Related structure data
Related structure data | 3q6x S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26834.170 Da / Num. of mol.: 2 / Fragment: LACTAMASE_B, RESIDUES 29-270 Source method: isolated from a genetically manipulated source Details: TIOPRONIN INHIBITOR BINDING / Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: C7C422, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 50 % / Description: NONE |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: FOR CRYSTALLIZATION, THE PURIFIED PROTEIN WAS CONCENTRATED TO 19.88 MG/ML. APO - NDM - 1 CRYSTALS WERE GROWN AT 25 C FOR 3 WEEKS USING THE HANGING - DROP VAPOUR DIFFUSION METHOD BY MIXING 0. ...Details: FOR CRYSTALLIZATION, THE PURIFIED PROTEIN WAS CONCENTRATED TO 19.88 MG/ML. APO - NDM - 1 CRYSTALS WERE GROWN AT 25 C FOR 3 WEEKS USING THE HANGING - DROP VAPOUR DIFFUSION METHOD BY MIXING 0.7UL OF PROTEIN SOLUTION WITH 1UL OF RESERVOIR BUFFER (24 % PEG 1500 AND 0.05 M TBG (SODIUM TARTRATE/BIS - TRIS/GLYCYLGLYCINE) PH 4) AND 0.3UL OF 1/10 DILUTION OF NDM - 1 CRYSTAL SEEDS STOCK. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99988 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99988 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.66 Å / Num. obs: 17411 / % possible obs: 100 % / Observed criterion σ(I): 1.89 / Redundancy: 9.2 % / Biso Wilson estimate: 41.11 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 12.17 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.89 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3Q6X 3q6x Resolution: 2.6→46.659 Å / SU ML: 0.33 / σ(F): 1.23 / Phase error: 25.1 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→46.659 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|