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Yorodumi- PDB-4gee: Pyrrolopyrimidine inhibitors of DNA gyrase B and topoisomerase IV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gee | ||||||
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Title | Pyrrolopyrimidine inhibitors of DNA gyrase B and topoisomerase IV, part I: structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity. | ||||||
Components | DNA gyrase subunit B | ||||||
Keywords | Isomerase/Isomerase inhibitor / ATP-binding / Nucleotide-binding / Topoisomerase / ATP-binding domain / DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings / 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 | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Bensen, D.C. / Chen, Z. / Tari, L.W. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity. Authors: Tari, L.W. / Trzoss, M. / Bensen, D.C. / Li, X. / Chen, Z. / Lam, T. / Zhang, J. / Creighton, C.J. / Cunningham, M.L. / Kwan, B. / Stidham, M. / Shaw, K.J. / Lightstone, F.C. / Wong, S.E. / ...Authors: Tari, L.W. / Trzoss, M. / Bensen, D.C. / Li, X. / Chen, Z. / Lam, T. / Zhang, J. / Creighton, C.J. / Cunningham, M.L. / Kwan, B. / Stidham, M. / Shaw, K.J. / Lightstone, F.C. / Wong, S.E. / Nguyen, T.B. / Nix, J. / Finn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gee.cif.gz | 58 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gee.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 4gee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/4gee ftp://data.pdbj.org/pub/pdb/validation_reports/ge/4gee | HTTPS FTP |
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-Related structure data
Related structure data | 4gfnC 4gglC 4hxwC 4hxzC 4hy1C 4hymC 4hypC 4hz0C 4hz5C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23835.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: gyrB, EF_0005 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q839Z1, EC: 5.99.1.3 |
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#2: Chemical | ChemComp-0WT / ( |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25% (w/v) PEG 1500, 3% (v/v) t-butanol, 20% (w/v) glycerol, 20 mM citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 |
Detector | Type: NOIR-1 / Detector: CCD / Date: Aug 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→34.19 Å / Num. all: 23876 / Num. obs: 23876 / % possible obs: 98.9 % |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3181 / Rsym value: 0.385 / % possible all: 98.9 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.19 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.795 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.315 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→34.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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