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- PDB-2gwa: Crystal Structure of a Complex Formed Between the DNA Holliday Ju... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gwa | ||||||||||||||||||||
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Title | Crystal Structure of a Complex Formed Between the DNA Holliday Junction and a Bis-Acridine Molecule. | ||||||||||||||||||||
![]() | 5'-D(*![]() DNA / DNA HOLLIDAY JUNCTION BIS-ACRIDINE | Function / homology | Chem-A4C / SPERMINE / DNA | ![]() Method | ![]() ![]() ![]() Brogden, A.L. / Hopcroft, N.H. / Cardin, C.J. / Searcey, M. | ![]() ![]() Title: Ligand bridging of the DNA Holliday junction: molecular recognition of a stacked-X four-way junction by a small molecule. Authors: Brogden, A.L. / Hopcroft, N.H. / Searcey, M. / Cardin, C.J. History |
Remark 600 | HETEROGEN HETEROGEN A4C 1 REPRESENTS ONE HALF OF THE LIGAND, THE OTHER HALF IS GENERATED BY THE ...HETEROGEN HETEROGEN A4C 1 REPRESENTS ONE HALF OF THE LIGAND, THE OTHER HALF IS GENERATED BY THE SYMMETRY OPERATION USED TO GENERATE THE BIOLOGICAL UNIT. THE MOLECULE AS A WHOLE LIES ON A CRYSTALLOGRAPHIC AXIS OF TWO-FOLD ROTATIONAL SYMMETRY. HENCE, IN THE ASYMMETRIC UNIT, ONLY HALF THE LIGAND IS PRESENT IN THE COORDINATE FILE SUBMITTED. LINKS ARE PROVIDED BETWEEN SYMMETRY RELATED CX6 ATOMS. | |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 28.6 KB | Display | ![]() |
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PDB format | ![]() | 16.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 690.8 KB | Display | ![]() |
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Full document | ![]() | 707.2 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nqsS S: Starting model for refinement |
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Similar structure data |
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Links
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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 UNIT IS GENERATED BY THE SYMMETRY OPERATION: -X, Y, -Z. |
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Components
#1: DNA chain | Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-A4C / | #3: Chemical | ChemComp-SPM / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40mM SODIUM CACODYLATE PH 7.0, 12mM SPERMINE, 10% MPD, WITH 35% MPD RESERVOIR., VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.806 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→6 Å / Num. all: 4960 / Num. obs: 4045 / % possible obs: 86.4 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 2.2 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 5.2 / Num. unique all: 4960 / % possible all: 86.4 |
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Processing
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Refinement | Starting model: PDB ENTRY 1NQS Resolution: 1.75→6 Å / Num. parameters: 2292 / Num. restraintsaints: 1970 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 572 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→6 Å
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Refine LS restraints |
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