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Open data
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Basic information
Entry | Database: PDB / ID: 7r6t | ||||||
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Title | Human EXOG complexed with dRP-containing DNA | ||||||
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![]() | DNA BINDING PROTEIN/DNA / Mitochondrial BER / endo/exonuclease / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / protein-containing complex / mitochondrion ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / protein-containing complex / mitochondrion / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Szymanski, M.R. / Yin, Y.W. | ||||||
![]() | ![]() Title: Human EXOG possesses strong AP hydrolysis activity Authors: Szymanski, M.R. / Yin, Y.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.3 KB | Display | ![]() |
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PDB format | ![]() | 163.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7r6vC ![]() 5t5cS S: Starting model for refinement 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules DCL
#1: Protein | Mass: 35444.203 Da / Num. of mol.: 3 / Mutation: H140A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y2C4, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters |
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-DNA chain , 2 types, 6 molecules FEMABK
#2: DNA chain | Mass: 2911.894 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The mismatch is due to a deoxyribose site. / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3343.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 16 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-NA / | #6: 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: 2.38 Å3/Da / Density % sol: 48.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 28% PEG 4K, 0.2 M Ammonium Acetate, 0.1 M Na Citrate tribasic dihydrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2021 |
Radiation | Monochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 26817 / % possible obs: 99 % / Redundancy: 6.4 % / CC1/2: 0.75 / Net I/σ(I): 2.7 |
Reflection shell | Resolution: 2.9→3.5 Å / Redundancy: 6.3 % / Num. unique obs: 2612 / CC1/2: 0.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5T5C Resolution: 2.9→37.97 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 92.6 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→37.97 Å
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Refine LS restraints |
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