+
Open data
-
Basic information
Entry | Database: PDB / ID: 7d5e | ||||||
---|---|---|---|---|---|---|---|
Title | Left-handed G-quadruplex containing two bulges | ||||||
![]() | 2xBulge-LHG4motif | ||||||
![]() | DNA / G-quadruplex / Bulge / Left-handed | ||||||
Function / homology | : / SPERMINE / DNA / DNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Das, P. / Maity, A. / Ngo, K.H. / Winnerdy, F.R. / Bakalar, B. / Mechulam, Y. / Schmitt, E. / Phan, A.T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Bulges in left-handed G-quadruplexes. Authors: Das, P. / Ngo, K.H. / Winnerdy, F.R. / Maity, A. / Bakalar, B. / Mechulam, Y. / Schmitt, E. / Phan, A.T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 77.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 393.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 394.2 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d5dC ![]() 7d5fC ![]() 4u5mS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 8872.649 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-SPM / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.43 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.08 M potassium chloride, 0.04 M sodium cacodylate trihydrate pH 7.0, 60% v/v -2-methyl-2,4-pentanediol and 0.012 M spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.296→29.093 Å / Num. obs: 31051 / % possible obs: 94.67 % / Redundancy: 6 % / Biso Wilson estimate: 11.81 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.073 / Rrim(I) all: 0.18 / Net I/σ(I): 6.86 |
Reflection shell | Resolution: 1.296→1.342 Å / Rmerge(I) obs: 1.203 / Num. unique obs: 2861 / CC1/2: 0.732 / Rpim(I) all: 0.589 / Rrim(I) all: 1.345 / % possible all: 90.68 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4U5M Resolution: 1.296→29.093 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.26 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.11 Å2 / Biso mean: 17.2102 Å2 / Biso min: 8.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.296→29.093 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|