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Yorodumi- PDB-3p5j: The structure of the human RNase H2 complex defines key interacti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p5j | ||||||
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Title | The structure of the human RNase H2 complex defines key interaction interfaces relevant to enzyme function and human disease | ||||||
Components |
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Keywords | HYDROLASE/REPLICATION / RNase H2 fold / triple beta-barrel / Nuclease that cleaves RNA/DNA hybrids / Proliferating Cell Nuclear Antigen (PCNA) and RNA/DNA hybrids / nucleus / HYDROLASE-REPLICATION complex | ||||||
Function / homology | Function and homology information ribonucleotide metabolic process / ribonuclease H2 complex / DNA replication, removal of RNA primer / regulation of DNA damage checkpoint / RNA catabolic process / ribonuclease H / mismatch repair / regulation of G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / RNA-DNA hybrid ribonuclease activity ...ribonucleotide metabolic process / ribonuclease H2 complex / DNA replication, removal of RNA primer / regulation of DNA damage checkpoint / RNA catabolic process / ribonuclease H / 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 / in utero embryonic development / negative regulation of gene expression / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.9 Å | ||||||
Authors | Bubeck, D. / Graham, S.C. / Jones, E.Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: The structure of the mammalian RNase H2 complex provides insight into RNA.NA hybrid processing to prevent immune dysfunction. Authors: Shaban, N.M. / Harvey, S. / Perrino, F.W. / Hollis, T. | ||||||
History |
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Remark 0 | THIS ENTRY 3P5J REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3KIOSF DETERMINED ...THIS ENTRY 3P5J REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3KIOSF DETERMINED BY AUTHORS OF THE PDB ENTRY 3KIO: N.Shaban,D.Harvey,F.W.Perrino,T.Hollis. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p5j.cif.gz | 219.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p5j.ent.gz | 173.6 KB | Display | PDB format |
PDBx/mmJSON format | 3p5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p5j_validation.pdf.gz | 452.7 KB | Display | wwPDB validaton report |
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Full document | 3p5j_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 3p5j_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3p5j_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/3p5j ftp://data.pdbj.org/pub/pdb/validation_reports/p5/3p5j | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33547.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnaseh2a, Rnasehi / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CWY8, ribonuclease H |
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#2: Protein | Mass: 37494.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnaseh2b, Dleu8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80ZV0 |
#3: Protein | Mass: 17848.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnaseh2c, Ayp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQ18 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.88 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3KIO. |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 62.11 Å2 |
-Processing
Software | Name: BUSTER / Version: 2.9.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD / Resolution: 2.9→24.61 Å / Cor.coef. Fo:Fc: 0.8969 / Cor.coef. Fo:Fc free: 0.8348 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: This is a re-refinement of the murine RNase H2 coordinates previously deposited by Shaban et al., 2010 (PDB ID 3KIO)
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Displacement parameters | Biso mean: 62.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.405 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→24.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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