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- PDB-2qkk: Human RNase H catalytic domain mutant D210N in complex with 14-me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qkk | ||||||
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Title | Human RNase H catalytic domain mutant D210N in complex with 14-mer RNA/DNA hybrid | ||||||
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![]() | HYDROLASE/DNA/RNA / RNase H / RNA/DNA hybrid / HYDROLASE-DNA-RNA COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nowotny, M. / Gaidamakov, S.A. / Ghirlando, R. / Cerritelli, S.M. / Crouch, R.J. / Yang, W. | ||||||
![]() | ![]() Title: Structure of Human RNase H1 Complexed with an RNA/DNA Hybrid: Insight into HIV Reverse Transcription Authors: Nowotny, M. / Gaidamakov, S.A. / Ghirlando, R. / Cerritelli, S.M. / Crouch, R.J. / Yang, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 421.4 KB | Display | ![]() |
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PDB format | ![]() | 329.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2qk9C ![]() 2qkbC ![]() 2kq9S C: citing same article ( 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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3 | ![]()
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6 | ![]()
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Unit cell |
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Components
-RNA chain / DNA chain / Protein , 3 types, 23 molecules CGKOTXDHLPUZABEFIJMNRSW
#1: RNA chain | Mass: 4382.659 Da / Num. of mol.: 6 / Source method: obtained synthetically #2: DNA chain | Mass: 4360.840 Da / Num. of mol.: 6 / Source method: obtained synthetically #3: Protein | Mass: 17104.279 Da / Num. of mol.: 11 / Fragment: C-terminal domain (residues 134-286) / Mutation: D210N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 189 molecules ![](data/chem/img/TRS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-TRS / | ||||||
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#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-MES / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.5 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 12% isopropanol, 0.2 M calcium acetate, 0.1 M MES, 0.1 M LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 54218 / Num. obs: 50322 / % possible obs: 92.8 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 3.2→3.3 Å / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2KQ9 Resolution: 3.2→30 Å / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 62.4 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→30 Å
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Refine LS restraints |
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