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Yorodumi- PDB-1fms: Structure of complex between cyclohexyl-bis-furamidine and d(CGCG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fms | ||||||||||||||||||
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Title | Structure of complex between cyclohexyl-bis-furamidine and d(CGCGAATTCGCG) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DNA-drug minor groove complex | Function / homology | Chem-D35 / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | Authors | Simpson, I.J. / Lee, M. / Kumar, A. / Boykin, D.W. / Neidle, S. | Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2000 | Title: DNA minor groove interactions and the biological activity of 2,5-bis-[4-(N-alkylamidino)phenyl] furans Authors: Simpson, I.J. / Lee, M. / Kumar, A. / Boykin, D.W. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fms.cif.gz | 29.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fms.ent.gz | 18.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fms_validation.pdf.gz | 397.2 KB | Display | wwPDB validaton report |
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Full document | 1fms_full_validation.pdf.gz | 402.2 KB | Display | |
Data in XML | 1fms_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 1fms_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/1fms ftp://data.pdbj.org/pub/pdb/validation_reports/fm/1fms | HTTPS FTP |
-Related 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 #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-D35 / | #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: 2.21 Å3/Da / Density % sol: 44.22 % | ||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: MgCl2 2ul 100mM, Spermine 1ul 10mM, Oligonucleotide 2ul 2mM, Drug 2ul 3mM, MPD 3ul 30% v/v, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→10 Å / Num. all: 5750 / Num. obs: 5492 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.035 |
-Processing
Software |
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Refinement | Resolution: 1.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Parkinson et al.
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.217 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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