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Yorodumi- PDB-3p56: The structure of the human RNase H2 complex defines key interacti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p56 | ||||||
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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 H 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 / regulation of G2/M transition of mitotic cell cycle / RNA nuclease activity / mismatch repair / 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 / regulation of G2/M transition of mitotic cell cycle / RNA nuclease activity / mismatch repair / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.06 Å | ||||||
Authors | Bubeck, D. / Graham, S.C. / Jones, E.Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The Structure of the Human RNase H2 Complex Defines Key Interaction Interfaces Relevant to Enzyme Function and Human Disease. Authors: Reijns, M.A. / Bubeck, D. / Gibson, L.C. / Graham, S.C. / Baillie, G.S. / Jones, E.Y. / Jackson, A.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p56.cif.gz | 396.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p56.ent.gz | 325.3 KB | Display | PDB format |
PDBx/mmJSON format | 3p56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p56_validation.pdf.gz | 482.7 KB | Display | wwPDB validaton report |
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Full document | 3p56_full_validation.pdf.gz | 492.9 KB | Display | |
Data in XML | 3p56_validation.xml.gz | 35 KB | Display | |
Data in CIF | 3p56_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/3p56 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/3p56 | HTTPS FTP |
-Related structure data
Related structure data | 3p5jC 3kioS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33343.820 Da / Num. of mol.: 2 / Mutation: D34A, D169A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEH2A, RNASEHI, RNHIA / Plasmid: polycistronic construct based on pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: O75792, ribonuclease H #2: Protein | Mass: 26699.691 Da / Num. of mol.: 2 / Fragment: RNASEH2B, UNP residues 2-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLEU8, RNASEH2B / Plasmid: polycistronic construct based on pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: Q5TBB1 #3: Protein | Mass: 17862.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AYP1, RNASEH2C / Plasmid: polycistronic construct based on pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: Q8TDP1 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG 3350, 0.1M bis-Tris pH6.5, 0.2M KNO3, vapor diffusion, sitting drop, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.06→30 Å / Num. obs: 13282 / % possible obs: 98.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.18 / Χ2: 1.483 / Net I/σ(I): 3.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: re-refined PDB ID: 3KIO Resolution: 4.06→30 Å / Cor.coef. Fo:Fc: 0.7988 / Cor.coef. Fo:Fc free: 0.7421 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 290.28 Å2 / Biso mean: 188.0547 Å2 / Biso min: 37.77 Å2
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Refine analyze | Luzzati coordinate error obs: 1.728 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.06→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.06→4.38 Å / Total num. of bins used: 7
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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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