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Yorodumi- PDB-4k4o: The DNA Gyrase B ATP binding domain of Enterococcus faecalis in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k4o | ||||||
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Title | The DNA Gyrase B ATP binding domain of Enterococcus faecalis in complex with a small molecule inhibitor | ||||||
Components | DNA gyrase subunit B | ||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / ATP-binding / Nucleotide-binding / Topoisomerase / ATP-binding domain / Isomerase-Isomerase inhibitor complex / cytosol | ||||||
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: 1.3 Å | ||||||
Authors | Bensen, D.C. / Akers-Rodriguez, S. / Lam, T. / Tari, L.W. | ||||||
Citation | Journal: To be Published Title: A new class of type IIA topoisomerase inhibitors with broad-spectrum antibacterial activity Authors: Tari, L.W. / Bensen, D.C. / Finn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k4o.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k4o.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 4k4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/4k4o ftp://data.pdbj.org/pub/pdb/validation_reports/k4/4k4o | HTTPS FTP |
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-Related structure data
Related structure data | 4kfgC 4geeS S: Starting model for refinement 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 / Fragment: UNP residues 18-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: EF_0005, gyrB / 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-DOO / |
#3: Chemical | ChemComp-TBU / |
#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: 2.18 Å3/Da / Density % sol: 43.69 % |
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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, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jan 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→43.58 Å / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.3→1.38 Å / % possible all: 97.6 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GEE Resolution: 1.3→43.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.661 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.05 / 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: 12.331 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→43.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.298→1.332 Å / Total num. of bins used: 20
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