+Open data
-Basic information
Entry | Database: PDB / ID: 6bcf | ||||||
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Title | I-LtrI G183A bound to cognate substrate (pre-cleavage complex) | ||||||
Components |
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Keywords | HYDROLASE/DNA / Nucleic Acid / HYDROLASE / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Leptographium truncatum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å | ||||||
Authors | Brown, C. / Zhang, K. / McMurrough, T.A. / Gloor, G.B. / Edgell, D.R. / Junop, M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases. Authors: McMurrough, T.A. / Brown, C.M. / Zhang, K. / Hausner, G. / Junop, M.S. / Gloor, G.B. / Edgell, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bcf.cif.gz | 344.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bcf.ent.gz | 261.5 KB | Display | PDB format |
PDBx/mmJSON format | 6bcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/6bcf ftp://data.pdbj.org/pub/pdb/validation_reports/bc/6bcf | HTTPS FTP |
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-Related structure data
Related structure data | 6bceC 6bcgC 6bciC 6bcnC 6bctC 3r7pS 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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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 36029.262 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptographium truncatum (fungus) / Gene: HEG fusion, rps3 / Production host: Escherichia coli (E. coli) / References: UniProt: C7SWF3 #2: DNA chain | Mass: 8042.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Leptographium truncatum (fungus) #3: DNA chain | Mass: 7931.144 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Leptographium truncatum (fungus) #4: Chemical | ChemComp-CA / |
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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: 2.39 Å3/Da / Density % sol: 48.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 7.0 20% W/V PEG2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→66.77 Å / Num. obs: 72648 / % possible obs: 98 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.9201→2.9585 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2 / Num. unique all: 4530 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3r7p Resolution: 2.92→38.992 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.92→38.992 Å
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Refine LS restraints |
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LS refinement shell |
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