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Open data
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Basic information
Entry | Database: PDB / ID: 3puf | ||||||
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Title | Crystal structure of human RNase H2 complex | ||||||
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![]() | HYDROLASE / RNase H fold / triple barrel fold / RNase H | ||||||
Function / homology | ![]() ribonucleotide metabolic process / ribonuclease H2 complex / DNA replication, removal of RNA primer / regulation of DNA damage checkpoint / RNA catabolic process / ribonuclease H / RNA nuclease activity / mismatch repair / regulation of G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation ...ribonucleotide metabolic process / ribonuclease H2 complex / DNA replication, removal of RNA primer / regulation of DNA damage checkpoint / RNA catabolic process / ribonuclease H / RNA nuclease activity / mismatch repair / regulation of G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / RNA-DNA hybrid ribonuclease activity / gene expression / fibroblast proliferation / DNA replication / in utero embryonic development / negative regulation of gene expression / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Figiel, M. / Chon, H. / Cerritelli, S.M. / Cybulska, M. / Crouch, R.J. / Nowotny, M. | ||||||
![]() | ![]() Title: The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutieres syndrome defects. Authors: Figiel, M. / Chon, H. / Cerritelli, S.M. / Cybulska, M. / Crouch, R.J. / Nowotny, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 650.9 KB | Display | ![]() |
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PDB format | ![]() | 525.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 560.6 KB | Display | ![]() |
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Full document | ![]() | 586.7 KB | Display | |
Data in XML | ![]() | 108.8 KB | Display | |
Data in CIF | ![]() | 151.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kioS 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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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33724.156 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 25780.783 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 18144.414 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M MgCl2, 15% PEG 3350, 0.1M Bis-Tris (pH 5.5), and 2mM reduced glutathione, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 63130 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 69.09 Å2 / Rmerge(I) obs: 0.107 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.2 / % possible all: 87.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KIO Resolution: 3.1→44.1 Å / Cor.coef. Fo:Fc: 0.9039 / Cor.coef. Fo:Fc free: 0.8611 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 64.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.524 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→44.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
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