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Open data
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Basic information
Entry | Database: PDB / ID: 7tqb | |||||||||
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Title | Crystal structure of monoclonal S9.6 Fab bound to DNA-RNA hybrid | |||||||||
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![]() | IMMUNE SYSTEM/DNA-RNA HYBRID / Antibody Fab DNA:RNA hybrid Nucleic Acid DNA:RNA hybrid binding protein / DNA-RNA HYBRID / IMMUNE SYSTEM-DNA-RNA HYBRID complex | |||||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10)![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Bou-Nader, C. / Zhang, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of R-loop recognition by the S9.6 monoclonal antibody. Authors: Bou-Nader, C. / Bothra, A. / Garboczi, D.N. / Leppla, S.H. / Zhang, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.2 KB | Display | ![]() |
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PDB format | ![]() | 159.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.9 KB | Display | ![]() |
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Full document | ![]() | 479.5 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tqaC ![]() 3tt1S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24972.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Cell line (production host): CHO / Production host: ![]() ![]() |
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#2: Antibody | Mass: 24124.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Cell line (production host): CHO / Production host: ![]() ![]() |
-RNA chain / DNA chain , 2 types, 2 molecules AB
#3: RNA chain | Mass: 4094.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 4000.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 37 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 1000 0.2 M sodium narrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→40.5 Å / Num. obs: 9509 / % possible obs: 98.7 % / Redundancy: 12.1 % / CC1/2: 0.841 / CC star: 0.956 / Net I/σ(I): 3.78 |
Reflection shell | Resolution: 3.02→3.13 Å / Mean I/σ(I) obs: 1.55 / Num. unique obs: 925 / CC1/2: 0.393 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TT1 Resolution: 3.1→37.091 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.3 Å2 / Biso mean: 30.6873 Å2 / Biso min: 12.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→37.091 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 12.6181 Å / Origin y: -28.8717 Å / Origin z: 12.3193 Å
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Refinement TLS group |
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