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- PDB-4gs2: DNA Holliday junction stabilized by iodine halogen bond. I1J cons... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gs2 | ||||||
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Title | DNA Holliday junction stabilized by iodine halogen bond. I1J construct in related reference. | ||||||
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![]() | DNA / DNA Holliday junction / halogen bond | ||||||
Function / homology | DNA![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ho, P.S. / Carter, M. | ||||||
![]() | ![]() Title: Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions. Authors: Carter, M. / Voth, A.R. / Scholfield, M.R. / Rummel, B. / Sowers, L.C. / Ho, P.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 21.3 KB | Display | ![]() |
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PDB format | ![]() | 13.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.8 KB | Display | ![]() |
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Full document | ![]() | 380.8 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gqdC ![]() 4greC ![]() 4gsgC ![]() 4gsiC ![]() 2orgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | -x,y,-z |
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Components
#1: DNA chain | Mass: 3172.874 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: synthetically engineered DNA sequence |
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#2: DNA chain | Mass: 3029.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetically engineered DNA sequence |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.65 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 7 Details: 0.7mM DNA, 25mM sodium cacodylate pH 7.0 buffer, 10-25mM calcium chloride, and 0.8-1.2mM spermine, equilibrated against a reservoir of 30-40% aqueous MPD, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 133 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 31, 2004 |
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→50 Å / Num. all: 4645 / Num. obs: 3432 / % possible obs: 73.9 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.4 Å2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ORG Resolution: 1.9→23.3 Å / Rfactor Rfree error: 0.014 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 378015 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.4 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.9687 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.95 Å2 / Biso mean: 31.4219 Å2 / Biso min: 15.72 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→23.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
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Xplor file |
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