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Yorodumi- PDB-5gkp: Crystal structure of the EndoG worm homologue CPS-6 H148A/F122A i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gkp | ||||||
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Title | Crystal structure of the EndoG worm homologue CPS-6 H148A/F122A in complex with DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / EndoG / mitochondria / endonuclease / non-specific nuclease / protein-DNA interactions / 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 / double-stranded DNA endonuclease activity / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / DNA catabolic process / RNA catabolic process / RNA endonuclease activity / DNA endonuclease activity / endonuclease activity / mitochondrial inner membrane ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / double-stranded DNA endonuclease activity / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / DNA catabolic process / RNA catabolic process / RNA endonuclease activity / DNA endonuclease activity / endonuclease activity / mitochondrial inner membrane / sequence-specific DNA binding / protein homodimerization activity / mitochondrion / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Lin, J.L. / Yuan, H.S. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer. Authors: Lin, J.L. / Wu, C.C. / Yang, W.Z. / Yuan, H.S. #1: Journal: J.BIOL.CHEM. / Year: 2012 Title: StructuralInsightsintoApoptoticDNADegradationbyCED-3 ProteaseSuppressor-6(CPS-6)fromCaenorhabditiselegans Authors: Lin, J.L. / 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 | 5gkp.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gkp.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 5gkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/5gkp ftp://data.pdbj.org/pub/pdb/validation_reports/gk/5gkp | HTTPS FTP |
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-Related structure data
Related structure data | 5gkcC 3s5bS C: citing same article (ref.) S: Starting model for refinement |
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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: 28697.721 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 63-305 / Mutation: H148A, F122A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: cps-6, C41D11.8 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: Q95NM6, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters #2: DNA chain | Mass: 2413.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: 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: 2.13 Å3/Da / Density % sol: 42.26 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 30% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 6, 2014 Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator, Toroidal Focusing Mirror |
Radiation | Monochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 25101 / % possible obs: 99.8 % / Redundancy: 6.2 % / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.27→2.35 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S5B Resolution: 2.3→19.783 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5 Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.783 Å
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Refine LS restraints |
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LS refinement shell |
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