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Open data
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Basic information
Entry | Database: PDB / ID: 5zkj | ||||||
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Title | Human EXOG-H140A in complex with RNA/DNA hybrid duplex | ||||||
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![]() | HYDROLASE/RNA/DNA / Enzyme-substrate complex / Mitochondrial exonuclease / HYDROLASE-RNA-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 | ![]() ![]() ![]() | ||||||
![]() | Wu, C.C. / Lin, J.L.J. / Yuan, H.S. | ||||||
![]() | ![]() Title: A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication. Authors: Wu, C.C. / Lin, J.L.J. / Yang-Yen, H.F. / Yuan, H.S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 282.9 KB | Display | ![]() |
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PDB format | ![]() | 223.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.1 KB | Display | ![]() |
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Full document | ![]() | 496.6 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zkiC ![]() 6iidC ![]() 5t4iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / RNA chain / DNA chain , 3 types, 6 molecules ABCEDF
#1: Protein | Mass: 39216.262 Da / Num. of mol.: 2 / 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 #2: RNA chain | Mass: 3867.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3623.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 53 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 22% PEG 400 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 20, 2017 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.798→30 Å / Num. obs: 25994 / % possible obs: 95.8 % / Redundancy: 1.9 % / CC1/2: 0.934 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.044 / Rrim(I) all: 0.066 / Χ2: 1.003 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.798→2.88 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.747 / Num. unique obs: 2202 / CC1/2: 0.706 / Rpim(I) all: 0.435 / Rrim(I) all: 0.64 / Χ2: 0.999 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5T4I Resolution: 2.798→28.434 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.798→28.434 Å
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Refine LS restraints |
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LS refinement shell |
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