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Yorodumi- PDB-3o3g: T. maritima RNase H2 in complex with nucleic acid substrate and c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o3g | ||||||
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Title | T. maritima RNase H2 in complex with nucleic acid substrate and calcium ions | ||||||
Components |
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Keywords | HYDROLASE/DNA-RNA hybrid / RNase H fold / nuclease / HYDROLASE-DNA-RNA hybrid complex | ||||||
Function / homology | Function and homology information ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / mismatch repair / RNA-DNA hybrid ribonuclease activity / manganese ion binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rychlik, M.P. / Chon, H. / Cerritelli, S.M. / Klimek, P. / Crouch, R.J. / Nowotny, M. | ||||||
Citation | Journal: Mol.Cell / Year: 2010 Title: Crystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage. Authors: Rychlik, M.P. / Chon, H. / Cerritelli, S.M. / Klimek, P. / Crouch, R.J. / Nowotny, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o3g.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o3g.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 3o3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/3o3g ftp://data.pdbj.org/pub/pdb/validation_reports/o3/3o3g | HTTPS FTP |
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-Related structure data
Related structure data | 3o3fSC 3o3hC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24683.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rnhB, TM_0915 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X017, ribonuclease H | ||
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#2: DNA chain | Mass: 3702.428 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: DNA/RNA hybrid | Mass: 3638.380 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.3 M CaCl2, 0.1 M Tris-HCl, 20% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 17131 / Num. obs: 16994 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3O3F Resolution: 2.1→28.75 Å / SU ML: 0.27 / σ(F): 0.11 / Phase error: 25.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.35 Å2 / ksol: 0.335 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.75 Å
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Refine LS restraints |
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LS refinement shell |
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