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- PDB-8vnt: Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8vnt | ||||||||||||
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Title | Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 1800s | ||||||||||||
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![]() | HYDROLASE/DNA / Intron encoded homing endonuclease I-PpoI / HYDROLASE / HYDROLASE-DNA complex | ||||||||||||
Function / homology | ![]() intron homing / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||||||||
Biological species | ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Chang, C. / Gao, Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s Authors: Chang, C. / Gao, Y. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.8 KB | Display | ![]() |
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PDB format | ![]() | 80.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vmoC ![]() 8vmpC ![]() 8vmqC ![]() 8vmrC ![]() 8vmsC ![]() 8vmtC ![]() 8vmuC ![]() 8vmvC ![]() 8vmwC ![]() 8vmxC ![]() 8vmyC ![]() 8vmzC ![]() 8vn0C ![]() 8vn1C ![]() 8vn2C ![]() 8vn3C ![]() 8vn4C ![]() 8vn5C ![]() 8vn6C ![]() 8vn7C ![]() 8vn8C ![]() 8vn9C ![]() 8vnaC ![]() 8vnbC ![]() 8vncC ![]() 8vndC ![]() 8vneC ![]() 8vnfC ![]() 8vngC ![]() 8vnhC ![]() 8vnjC ![]() 8vnkC ![]() 8vnlC ![]() 8vnmC ![]() 8vnnC ![]() 8vnoC ![]() 8vnpC ![]() 8vnqC ![]() 8vnrC ![]() 8vnsC ![]() 8vnuC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 , 2 types, 4 molecules CDcd
#1: DNA chain | Mass: 3916.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: DNA chain | Mass: 2475.655 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 17680.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q94702, Hydrolases; Acting on ester bonds |
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-Non-polymers , 4 types, 411 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ZN / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M Sodium Malonate, PEG 3350, 0.1 M MES / PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 26, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.62→33.02 Å / Num. obs: 165081 / % possible obs: 99.6 % / Redundancy: 20.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.101 / Net I/σ(I): 16.69 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→33.02 Å
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Refine LS restraints |
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LS refinement shell |
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