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Yorodumi- PDB-1vaq: Crystal structure of the Mg2+-(chromomycin A3)2-d(TTGGCCAA)2 comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vaq | ||||||||||||||||||||||||||
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Title | Crystal structure of the Mg2+-(chromomycin A3)2-d(TTGGCCAA)2 complex reveals GGCC binding specificity of the drug dimer chelated by metal ion | ||||||||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Chromomycin A3 / MAD / DNA duplex / GGCC site / DNA kink / CD spectra | Function / homology | Chem-CPH / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | Authors | Hou, M.H. / Robinson, H. / Gao, Y.G. / Wang, A.H.-J. | Citation | Journal: Nucleic Acids Res. / Year: 2004 | Title: Crystal structure of the [Mg2+-(chromomycin A3)2]-d(TTGGCCAA)2 complex reveals GGCC binding specificity of the drug dimer chelated by a metal ion Authors: Hou, M.H. / Robinson, H. / Gao, Y.G. / Wang, A.H.-J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vaq.cif.gz | 45.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vaq.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 1vaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vaq_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 1vaq_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 1vaq_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1vaq_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/1vaq ftp://data.pdbj.org/pub/pdb/validation_reports/va/1vaq | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-DNA chain , 1 types, 4 molecules ABCD
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: The synthetic DNA oligonucleotides were purified by gel electrophoresis. Source: (synth.) synthetic construct (others) |
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-Sugars , 2 types, 8 molecules
#2: Polysaccharide | 2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H- ...2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate Source method: isolated from a genetically manipulated source #3: Polysaccharide | 3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol- ...3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 289 molecules
#4: Chemical | #5: Chemical | ChemComp-CPH / ( #6: 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: 1.79 Å3/Da / Density % sol: 30.91 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: sodium-cacodylate, MgCl2, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.5432 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5432 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 7815 / Redundancy: 6 % / Rmerge(I) obs: 0.0055 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 10 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å /
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