[English] 日本語

- PDB-7klp: Crystal structure of a three-tetrad, parallel, K+ stabilized huma... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7klp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a three-tetrad, parallel, K+ stabilized human telomeric G-quadruplex | ||||||
![]() | telomeric DNA | ||||||
![]() | DNA / three-quartets / Parallel / G-quadruplex / Propeller Loops / human telomeric DNA | ||||||
Function / homology | : / DNA / DNA (> 10)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yatsunyk, L.A. / Li, K.S. / Chen, E.V. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Water spines and networks in G-quadruplex structures. Authors: Li, K. / Yatsunyk, L. / Neidle, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2023 Title: Crystal structure of a three-tetrad, parallel, K + -stabilized human telomeric G-quadruplex at 1.35 angstrom resolution. Authors: Chen, E.V. / Nicoludis, J.M. / Powell, B.M. / Li, K.S. / Yatsunyk, L.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 65 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 40.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 700.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 700.8 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fxmS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: DNA chain | Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-K / #3: Chemical | ChemComp-P6G / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.1 % / Description: small square bipyramides |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 50 mM Li Cac pH 7.2, 200 mM KCl, 500 mM (NH4)2SO4, 23% PEG400 |
-Data collection
Diffraction | Mean temperature: 196 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→49.17 Å / Num. obs: 32545 / % possible obs: 99.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 19.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.017 / Rrim(I) all: 0.051 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.34→1.36 Å / Redundancy: 8.2 % / Rmerge(I) obs: 6.026 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 809 / CC1/2: 0.32 / Rpim(I) all: 2.187 / Rrim(I) all: 6.423 / % possible all: 91.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4FXM Resolution: 1.35→42.31 Å / SU ML: 0.1627 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.4905 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→42.31 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|