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- PDB-5wjr: High resolution native hexamer DNA and RNA hybrid in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wjr | ||||||
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Title | High resolution native hexamer DNA and RNA hybrid in complex with RNase H catalytic domain D132N mutant | ||||||
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![]() | HYDROLASE / 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. / Huang, Z. | ||||||
![]() | ![]() Title: Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate Authors: Fang, Z. / Dantsu, Y. / Chen, C. / Zhang, W. / 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 | ![]() | 55.2 KB | Display | ![]() |
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PDB format | ![]() | 33.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hg8C ![]() 3ijkC ![]() 3ltuC ![]() 5usaC ![]() 5useC ![]() 5usgC ![]() 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: 1824.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Protein | Mass: 16329.478 Da / Num. of mol.: 1 / Fragment: residues 59-196 / 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: 2.46 Å3/Da / Density % sol: 50.08 % |
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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: 1.7→61.79 Å / Num. obs: 20483 / % possible obs: 92.1 % / Redundancy: 5.8 % / Rpim(I) all: 0.033 / Χ2: 0.981 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1081 / CC1/2: 0.944 / Rpim(I) all: 0.136 / Χ2: 0.921 / % possible all: 53.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2G8U Resolution: 1.7→61.79 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 2.24 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.121 / 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: 15.648 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→61.79 Å
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Refine LS restraints |
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