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- PDB-4h8k: Crystal structure of LC11-RNase H1 in complex with RNA/DNA hybrid -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h8k | ||||||
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Title | Crystal structure of LC11-RNase H1 in complex with RNA/DNA hybrid | ||||||
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![]() | Hydrolase/DNA/RNA / RNase H / Ribonuclease H RNA DNA Hybrid / Hydrolase / Ribonuclease H / Hydrolase-DNA-RNA complex | ||||||
Function / homology | ![]() ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding Similarity search - Function | ||||||
Biological species | uncultured organism (environmental samples) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nguyen, T.N. / You, D.J. / Matsumoto, H. / Kanaya, E. / Kanaya, S. | ||||||
![]() | ![]() Title: Crystal structure of metagenome-derived LC11-RNase H1 in complex with RNA/DNA hybrid Authors: Nguyen, T.N. / You, D.J. / Matsumoto, H. / Kanaya, E. / Koga, Y. / Kanaya, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.3 KB | Display | ![]() |
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PDB format | ![]() | 61.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3u3gS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15630.956 Da / Num. of mol.: 2 / Mutation: D77N Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured organism (environmental samples) Plasmid: pET25b / Production host: ![]() ![]() #2: RNA chain | | Mass: 4382.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in bacteria #3: DNA chain | | Mass: 4360.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in bacteria #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M ammonium acetate, 0.1M Tris, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Nov 13, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 17868 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 42.556 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3U3G Resolution: 2.3→38.28 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.64 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.349 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.048 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→38.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.299→2.359 Å / Total num. of bins used: 20
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