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Yorodumi- PDB-360d: STRUCTURE OF 2,5-BIS{[4-(N-ETHYLAMIDINO)PHENYL]}FURAN COMPLEXED T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 360d | ||||||||||||||||||||
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Title | STRUCTURE OF 2,5-BIS{[4-(N-ETHYLAMIDINO)PHENYL]}FURAN COMPLEXED TO 5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'. A MINOR GROOVE DRUG COMPLEX, SHOWING PATTERNS OF GROOVE HYDRATION | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | Chem-BPF / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | Authors | Guerri, A. / Simpson, I.J. / Neidle, S. | Citation | Journal: Nucleic Acids Res. / Year: 1998 | Title: Visualisation of extensive water ribbons and networks in a DNA minor-groove drug complex. Authors: Guerri, A. / Simpson, I.J. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 360d.cif.gz | 28.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb360d.ent.gz | 19.2 KB | Display | PDB format |
PDBx/mmJSON format | 360d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 360d_validation.pdf.gz | 573 KB | Display | wwPDB validaton report |
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Full document | 360d_full_validation.pdf.gz | 577.3 KB | Display | |
Data in XML | 360d_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 360d_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/60/360d ftp://data.pdbj.org/pub/pdb/validation_reports/60/360d | HTTPS FTP |
-Related structure data
Related structure data | 289dS 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-BPF / | #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: 2.18 Å3/Da / Density % sol: 43.48 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 288.0K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7 / 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 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.85→7 Å / Num. obs: 5634 / % possible obs: 91.44 % / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.022 / Net I/σ(I): 33.18 |
Reflection shell | Resolution: 1.854→1.9 Å / Mean I/σ(I) obs: 14.67 / % possible all: 80.7 |
Reflection | *PLUS % possible obs: 96.2 % / Num. measured all: 36613 / Rmerge(I) obs: 0.034 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NDB ENTRY GDL045 (PDB: 289D) Resolution: 1.85→7 Å / Num. parameters: 2904 / Num. restraintsaints: 3734 / Cross valid method: NONE / σ(F): 4 StereochEM target val spec case: STEREOCHEMISTRY OF LIGAND FROM MM CALCULATIONS Stereochemistry target values: PARKINSON ET AL.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 | ||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 260 / Occupancy sum non hydrogen: 733 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→7 Å
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 7 Å / σ(F): 4 / Rfactor obs: 0.169 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.17 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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