+Open data
-Basic information
Entry | Database: PDB / ID: 6iid | ||||||
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Title | Human EXOG-H140A in complex with RNA-DNA chimeric duplex | ||||||
Components |
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Keywords | HYDROLASE/DNA / Enzyme-substrate complex / Mitochondrial exonuclease / HYDROLASE-DNA complex / DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.986 Å | ||||||
Authors | Wu, C.C. / Lin, J.L.J. / Yuan, H.S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iid.cif.gz | 496.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iid.ent.gz | 404.8 KB | Display | PDB format |
PDBx/mmJSON format | 6iid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iid_validation.pdf.gz | 526 KB | Display | wwPDB validaton report |
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Full document | 6iid_full_validation.pdf.gz | 537.7 KB | Display | |
Data in XML | 6iid_validation.xml.gz | 41.2 KB | Display | |
Data in CIF | 6iid_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/6iid ftp://data.pdbj.org/pub/pdb/validation_reports/ii/6iid | HTTPS FTP |
-Related structure data
Related structure data | 5zkiSC 5zkjC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39216.262 Da / Num. of mol.: 4 / Mutation: H140A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EXOG, ENDOGL1, ENDOGL2, ENGL / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS References: UniProt: Q9Y2C4, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters #2: DNA/RNA hybrid | Mass: 3735.416 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3623.368 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.2 M magnesium formate dehydrate and 20% [w/v] PEG 3350 PH range: 6.6-7.2 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 3, 2018 |
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: 2.986→30 Å / Num. obs: 30771 / % possible obs: 96.7 % / Redundancy: 1.9 % / CC1/2: 0.941 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.085 / Rrim(I) all: 0.12 / Χ2: 0.999 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 2246 / CC1/2: 0.855 / Rpim(I) all: 0.432 / Rrim(I) all: 0.611 / Χ2: 1.008 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZKI Resolution: 2.986→29.834 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.986→29.834 Å
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Refine LS restraints |
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LS refinement shell |
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