+Open data
-Basic information
Entry | Database: PDB / ID: 5zki | ||||||
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Title | Human EXOG-H140A in complex with duplex DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / Enzyme-substrate complex / Mitochondrial exonuclease / HYDROLASE-DNA complex | ||||||
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 / mitochondrial inner membrane / nucleic acid binding / 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 / mitochondrial inner membrane / nucleic acid binding / protein-containing complex / mitochondrion / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.321 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 | 5zki.cif.gz | 283.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zki.ent.gz | 224.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/5zki ftp://data.pdbj.org/pub/pdb/validation_reports/zk/5zki | HTTPS FTP |
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-Related structure data
Related structure data | 5zkjC 6iidC 4a1nS 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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Unit cell |
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-Components
#1: Protein | Mass: 39216.262 Da / Num. of mol.: 2 / 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 chain | Mass: 3663.392 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | #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: 2.33 Å3/Da / Density % sol: 47.17 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M BIS-Tris pH 6.5, 20% w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 1, 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: 2.32→30 Å / Num. obs: 38137 / % possible obs: 99.8 % / Redundancy: 7 % / CC1/2: 0.986 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Χ2: 0.999 / Net I/σ(I): 19.49 |
Reflection shell | Resolution: 2.32→2.37 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.794 / Num. unique obs: 2468 / CC1/2: 0.935 / Rpim(I) all: 0.194 / Rrim(I) all: 0.517 / Χ2: 1.005 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4A1N Resolution: 2.321→29.619 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.321→29.619 Å
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Refine LS restraints |
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LS refinement shell |
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