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Yorodumi- PDB-6vrd: Crystal structure of RNase H/RNA/PS-ASO complex at an atomic level -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vrd | ||||||
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Title | Crystal structure of RNase H/RNA/PS-ASO complex at an atomic level | ||||||
Components |
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Keywords | HYDROLASE/RNA / RNase H / Complex / RNA / ASO / DNA / HYDROLASE / HYDROLASE-RNA complex | ||||||
Function / homology | Function and homology information DNA replication, removal of RNA primer / RNA catabolic process / ribonuclease H / RNA nuclease activity / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / magnesium ion binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.299 Å | ||||||
Authors | Cho, Y.-J. / Butler, D. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of RNase H/RNA/PS-ASO complex at an atomic level Authors: Cho, Y.-J. / Butler, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vrd.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vrd.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/6vrd ftp://data.pdbj.org/pub/pdb/validation_reports/vr/6vrd | HTTPS FTP |
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-Related structure data
Related structure data | 8swbC 2qk9S 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33218.457 Da / Num. of mol.: 1 / Mutation: D210N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEH1, RNH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60930, ribonuclease H |
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-RNA chain , 2 types, 2 molecules BC
#2: RNA chain | Mass: 6614.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#3: RNA chain | Mass: 6637.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 355 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8 M Ammonium sulphate, 0.1 M citrate pH 4.0 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.299→35.133 Å / Num. obs: 65937 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 12.67 |
Reflection shell | Resolution: 1.299→1.346 Å / Num. unique obs: 6385 / CC1/2: 0.397 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2qk9 Resolution: 1.299→35.133 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.01 Å2 / Biso mean: 23.5414 Å2 / Biso min: 11.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.299→35.133 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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