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Yorodumi- PDB-6grb: eukaryotic junction-resolving enzyme GEN-1 binding with Potassium -
+Open data
-Basic information
Entry | Database: PDB / ID: 6grb | ||||||
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Title | eukaryotic junction-resolving enzyme GEN-1 binding with Potassium | ||||||
Components |
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Keywords | DNA / 4-way Holiday Junction / Resolvase / DNA recombination / GEN1 / H2TH / Potassium | ||||||
Function / homology | Function and homology information crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / DNA repair / metal ion binding Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Lilley, D.M.J. / Liu, Y. / Freeman, D.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1. Authors: Liu, Y. / Freeman, A.D. / Declais, A.C. / Lilley, D.M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6grb.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6grb.ent.gz | 153.8 KB | Display | PDB format |
PDBx/mmJSON format | 6grb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6grb_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6grb_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6grb_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 6grb_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/6grb ftp://data.pdbj.org/pub/pdb/validation_reports/gr/6grb | HTTPS FTP |
-Related structure data
Related structure data | 6grcC 6grdC 5cnqS 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: 58734.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Gene: CTHT_0007290 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RYN2 | ||
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#2: DNA chain | Mass: 4712.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
#3: DNA chain | Mass: 4748.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.43 % |
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Crystal grow | Temperature: 280 K / Method: evaporation / Details: HEPES pH 7.0 20% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.975 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→84.84 Å / Num. obs: 26441 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 63.42 Å2 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.4→2.53 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CNQ Resolution: 2.4→69.227 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.54 Å2 / Biso mean: 76.1223 Å2 / Biso min: 45.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→69.227 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 16.7412 Å / Origin y: -24.4044 Å / Origin z: -15.5058 Å
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Refinement TLS group |
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