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Yorodumi- PDB-8c41: High resolution structure of the Streptococcus pneumoniae topoiso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c41 | ||||||
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Title | High resolution structure of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin | ||||||
Components |
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Keywords | ISOMERASE / PROTEIN-DNA CLEAVAGE COMPLEX / TOPOISOMERASE IIA / DELAFLOXACIN / TOPOISOMERASE IV-DNA-ANTIBIOTIC COMPLEX | ||||||
Function / homology | delafloxacin / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) DNA molecule (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 Å | ||||||
Authors | Najmudin, S. / Pan, X.S. / Wang, B. / Chayen, N.E. / Fisher, L.M. / Sanderson, M.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: The nature of the molecular interactions at high resolution of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin. Authors: Najmudin, S. / Pan, X.S. / Wang, B. / Chayen, N.E. / Fisher, L.M. / Sanderson, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c41.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8c41.ent.gz | 963.4 KB | Display | PDB format |
PDBx/mmJSON format | 8c41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c41_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 8c41_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 8c41_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 8c41_validation.cif.gz | 81 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/8c41 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/8c41 | HTTPS FTP |
-Related structure data
Related structure data | 8qmbC 8qmcC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 84211.422 Da / Num. of mol.: 2 / Mutation: Insertion of His at postion 648 Source method: isolated from a genetically manipulated source Details: The fused TOPOISOMERASE IV CLEAVAGE COMPLEX comprises the C-terminal domain of the ParE30 domain (residues 415-647), a His insert at position 648 and the N-terminal domain of ParC55 (residues 1001-1486) Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: 7785 / Gene: SP_0852-SP_0855 / Plasmid: PET29A / Production host: Escherichia coli (E. coli) / References: EC: 5.99.1.- |
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-DNA chain , 4 types, 4 molecules EFGH
#2: DNA chain | Mass: 2121.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) |
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#3: DNA chain | Mass: 3348.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cleaved from the E18 mer oligo AGTCATTCATGACCTTGGT / Source: (synth.) DNA molecule (others) |
#4: DNA chain | Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) |
#5: DNA chain | Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) |
-Non-polymers , 5 types, 431 molecules
#6: Chemical | #7: Chemical | ChemComp-MG / #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 4.24 Å3/Da / Density % sol: 71 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.5% Tacsimate, 50 mM Na Cacodylate, 62.5 mM KCl, 7.5 mM MgCl2, 4-7.5% Isopropanol. 30% MPD as cryoprotectant PH range: 6.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.393→115.01 Å / Num. obs: 70836 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 60.8 % / CC1/2: 1 / Rmerge(I) obs: 0.564 / Rpim(I) all: 0.073 / Rrim(I) all: 0.569 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.394→2.689 Å / Redundancy: 49.5 % / Rmerge(I) obs: 4.363 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3517 / CC1/2: 0.83 / Rpim(I) all: 0.62 / Rrim(I) all: 4.483 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.393→115.01 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.175 / SU B: 14.946 / SU ML: 0.187 / Average fsc free: 0.9534 / Average fsc work: 0.9697 / Cross valid method: FREE R-VALUE / ESU R: 0.492 / ESU R Free: 0.307 Details: Hydrogens have been added in their riding positions
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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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.207 Å2
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Refinement step | Cycle: LAST / Resolution: 2.393→115.01 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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