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Yorodumi- PDB-4kqv: Topoisomerase iv atp binding domain of francisella tularensis in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kqv | ||||||
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Title | Topoisomerase iv atp binding domain of francisella tularensis in complex with a small molecule inhibitor | ||||||
Components | Topoisomerase IV, subunit B | ||||||
Keywords | ISOMERASE / ATP-binding / Nucleotide-binding / Topoisomerase / ATP-binding domain / DNA gyrase negatively supercoils closed circular double-stranded DNA | ||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. holarctica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 | 4kqv.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kqv.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/4kqv ftp://data.pdbj.org/pub/pdb/validation_reports/kq/4kqv | HTTPS FTP |
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-Related structure data
Related structure data | 4ksgC 4kshC 4ktnC 4hy1S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43950.766 Da / Num. of mol.: 2 / Fragment: unp residues 18-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. holarctica (bacteria) Strain: LVS Gene: DNA TOPOISOMERASE IV SUBUNIT B PARE, FTL_1726, FTL_1726; Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2A1P5, UniProt: A0A0J9WZF0*PLUS, EC: 5.99.1.3 #2: Chemical | ChemComp-IOD / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.4 Details: 10% PEG 4000, 10% ISOPROPANOL, 100 MM CITRATE, pH 5.4, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Mar 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→66.06 Å / Num. all: 142179 / Num. obs: 40074 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.076 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HY1 Resolution: 2.38→66.06 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.856 / SU B: 7.204 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.253 / 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: 57.886 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→66.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.383→2.445 Å / Total num. of bins used: 20
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