[English] 日本語
Yorodumi- PDB-3g7e: Crystal structure of E. coli Gyrase B co-complexed with PROP-2-YN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g7e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E. coli Gyrase B co-complexed with PROP-2-YN-1-YL {[5-(4-PIPERIDIN-1-YL-2-PYRIDIN-3-YL-1,3-THIAZOL-5-YL)-1H-PYRAZOL-3-YL]METHYL}CARBAMATE inhibitor | ||||||
Components | DNA gyrase subunit B | ||||||
Keywords | Isomerase/Isomerase inhibitor / ISOMERASE / Isomerase-Isomerase inhibitor complex | ||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wei, Y. / Charifson, P. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Discovery of pyrazolthiazoles as novel and potent inhibitors of bacterial gyrase. Authors: Ronkin, S.M. / Badia, M. / Bellon, S. / Grillot, A.L. / Gross, C.H. / Grossman, T.H. / Mani, N. / Parsons, J.D. / Stamos, D. / Trudeau, M. / Wei, Y. / Charifson, P.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3g7e.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3g7e.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 3g7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/3g7e ftp://data.pdbj.org/pub/pdb/validation_reports/g7/3g7e | HTTPS FTP |
---|
-Related structure data
Related structure data | 3g75C 3g7bC 1s14S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22299.082 Da / Num. of mol.: 1 / Fragment: residues 15-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECs4634 / Production host: Escherichia coli (E. coli) / References: UniProt: C3SLN3, EC: 5.99.1.3 |
---|---|
#2: Chemical | ChemComp-B46 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.72 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: hanging drop, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 21, 2006 / Details: mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 13863 / Num. obs: 13724 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.2→2.3 Å / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S14 Resolution: 2.2→19.81 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3885254.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.6705 Å2 / ksol: 0.34316 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.81 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|