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- PDB-5w7o: 2-Se-T4-DNA and native RNA hybrid in complex with RNase H catalyt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w7o | ||||||
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Title | 2-Se-T4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant | ||||||
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![]() | HYDROLASE/DNA/RNA / HYDROLASE-DNA-RNA complex | ||||||
Function / homology | ![]() ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fang, Z. / Yang, F. / Huang, Z. | ||||||
![]() | ![]() Title: 2-Se-T-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant Authors: Fang, Z. / Yang, F. / Huang, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.6 KB | Display | ![]() |
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PDB format | ![]() | 33.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.8 KB | Display | ![]() |
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Full document | ![]() | 445.2 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5us2C ![]() 2g8uS S: Starting model for refinement C: citing same article ( |
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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: RNA chain | Mass: 1875.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: DNA chain | Mass: 1887.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Protein | Mass: 15243.206 Da / Num. of mol.: 1 / Fragment: residues 62-193 / Mutation: D132N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125 Gene: rnhA, BH0863 / Production host: ![]() ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.5, 12%(w/v) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 18994 / % possible obs: 89.6 % / Redundancy: 3.3 % / Rpim(I) all: 0.024 / Χ2: 0.743 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.75→1.81 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1030 / CC1/2: 0.927 / Rpim(I) all: 0.144 / Χ2: 0.876 / % possible all: 54.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2g8u Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.349 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.124 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.647 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→50 Å
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Refine LS restraints |
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