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- PDB-6m5b: X-ray crystal structure of cyclic-PIP and DNA complex in a revers... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m5b | |||||||||||||||||||||||||||||||
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Title | X-ray crystal structure of cyclic-PIP and DNA complex in a reverse binding orientation | |||||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / PIP | Function / homology | Chem-S7E / DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Abe, K. / Hirose, Y. / Eki, H. / Takeda, K. / Bando, T. / Endo, M. / Sugiyama, H. | Funding support | | ![]()
![]() ![]() Title: X-ray Crystal Structure of a Cyclic-PIP-DNA Complex in the Reverse-Binding Orientation. Authors: Abe, K. / Hirose, Y. / Eki, H. / Takeda, K. / Bando, T. / Endo, M. / Sugiyama, H. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.5 KB | Display | ![]() |
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PDB format | ![]() | 12.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 655.8 KB | Display | ![]() |
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Full document | ![]() | 657.5 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 4.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Components
-DNA chain , 1 types, 1 molecules A
#1: DNA chain | Mass: 3124.888 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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-Non-polymers , 5 types, 50 molecules ![](data/chem/img/S7E.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-S7E / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12.5% polyethylene glycol monomethyl ether 550, 2.5 mM magnesium chloride hexahydrate, 25 mM HEPES sodium, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 16.7 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→41.118 Å / Num. obs: 14247 / % possible obs: 98.6 % / Redundancy: 14.328 % / Biso Wilson estimate: 23.982 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.054 / Χ2: 1.742 / Net I/σ(I): 26.37 / Num. measured all: 204128 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 43.15 Å2 / Biso mean: 21.7689 Å2 / Biso min: 13.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.501→29.074 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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