+Open data
-Basic information
Entry | Database: PDB / ID: 4u8b | ||||||||||||||||||||||||||||
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Title | Crystal structure of D(CGCGAATTCGCG)2 complexed with BPH-1358 | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA/ANTIBIOTIC / Antibacterial Agents / Bisamidines / Minor Groove Binders / Models / Molecular / Nucleic Acid Conformation / Oligodeoxyribonucleotides / DNA-ANTIBIOTIC complex | Function / homology | Chem-3F2 / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | Authors | Zhu, W. / Oldfield, E. | Funding support | United States, 1items |
Citation | Journal: J.Med.Chem. / Year: 2015 | Title: Antibacterial drug leads: DNA and enzyme multitargeting. Authors: Zhu, W. / Wang, Y. / Li, K. / Gao, J. / Huang, C.H. / Chen, C.C. / Ko, T.P. / Zhang, Y. / Guo, R.T. / Oldfield, E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u8b.cif.gz | 28.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u8b.ent.gz | 16.8 KB | Display | PDB format |
PDBx/mmJSON format | 4u8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u8b_validation.pdf.gz | 625.7 KB | Display | wwPDB validaton report |
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Full document | 4u8b_full_validation.pdf.gz | 631.2 KB | Display | |
Data in XML | 4u8b_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 4u8b_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/4u8b ftp://data.pdbj.org/pub/pdb/validation_reports/u8/4u8b | HTTPS FTP |
-Related structure data
Related structure data | 3wyiC 3wyjC 4u82C 4u8aC 4u8cC 436dS C: citing same article (ref.) S: Starting model for refinement |
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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: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-3F2 / | #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: 2.09 Å3/Da / Density % sol: 41.08 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6.9 Details: 40 mM sodium cacodylate, pH 6.9, 50 mM Mg(OAc)2, 6 mM spermine-4HCl, 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97857 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.31→50 Å / Num. obs: 15205 / % possible obs: 98.7 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.076 / Χ2: 1.063 / Net I/av σ(I): 29.844 / Net I/σ(I): 10.8 / Num. measured all: 203452 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 436D Resolution: 1.31→16.87 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.077 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 61.98 Å2 / Biso mean: 21.421 Å2 / Biso min: 11.55 Å2
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Refinement step | Cycle: final / Resolution: 1.31→16.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.31→1.344 Å / Total num. of bins used: 20
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