+Open data
-Basic information
Entry | Database: PDB / ID: 7r6v | ||||||
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Title | Human EXOG complexed with dRP-containing DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Mitochondrial BER / endo/exonuclease / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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: 2.16 Å | ||||||
Authors | Szymanski, M.R. / Yin, Y.W. | ||||||
Citation | Journal: To Be Published Title: Human EXOG possesses strong AP hydrolysis activity Authors: Szymanski, M.R. / Yin, Y.W. #1: Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r6v.cif.gz | 584.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r6v.ent.gz | 452.7 KB | Display | PDB format |
PDBx/mmJSON format | 7r6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/7r6v ftp://data.pdbj.org/pub/pdb/validation_reports/r6/7r6v | HTTPS FTP |
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-Related structure data
Related structure data | 7r6tC 5t5cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 4 molecules DEGI
#1: Protein | Mass: 35511.270 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 / Production host: Escherichia coli (E. coli) 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, 8 molecules FHJKBALM
#2: DNA chain | Mass: 3061.003 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3656.407 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 399 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.31 Å3/Da / Density % sol: 46.77 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 28% PEG 4K, 0.2 M Ammonium Sulphate, 0.1 M Na Acetate Trihydrate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→50 Å / Num. obs: 79362 / % possible obs: 97 % / Redundancy: 1.8 % / CC1/2: 0.75 / Net I/σ(I): 1.5 |
Reflection shell | Resolution: 2.16→2.5 Å / Num. unique obs: 7224 / CC1/2: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T5C Resolution: 2.16→50 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 55.65 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.16→50 Å
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Refine LS restraints |
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