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Yorodumi- PDB-2gjb: Crosslinking of DNA duplexes: X-ray crystal structure of an unsub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gjb | ||||||||||||||||||
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Title | Crosslinking of DNA duplexes: X-ray crystal structure of an unsubstituted bisacridine with the oligonucleotide d(CGTACG) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DNA duplex / bis-intercalator | Function / homology | Chem-BMO / : / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | Authors | Gan, Y. / Cardin, C.J. / Denny, W.A. | Citation | Journal: To be Published | Title: Crosslinking of DNA duplexes: X-ray crystal structure of an unsubstituted bisacridine with oligonucleotide d(CGTACG) Authors: Gan, Y. / Cardin, C.J. / Denny, W.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gjb.cif.gz | 14.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gjb.ent.gz | 8.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gjb_validation.pdf.gz | 695.1 KB | Display | wwPDB validaton report |
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Full document | 2gjb_full_validation.pdf.gz | 697.9 KB | Display | |
Data in XML | 2gjb_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 2gjb_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/2gjb ftp://data.pdbj.org/pub/pdb/validation_reports/gj/2gjb | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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Details | The second part of the biological assembly is generated by the two fold axis |
-Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-BMO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.53 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: The crystals grow in ten days from sitting drops containing 2mM DNA, 12mM spermine, 80mM strontium chloride, 20mM magnesium chloride, 10%MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→22.3 Å / Num. obs: 1472 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 20.1 % / Biso Wilson estimate: 57.431 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 49.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 9 / Num. unique all: 204 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NDB ENTRY DD0018 Resolution: 2.2→8 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.648 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.613 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.253 Å / Total num. of bins used: 20
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