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Yorodumi- PDB-2g8k: B. halodurans RNase H catalytic domain D192N mutant in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g8k | ||||||
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Title | B. halodurans RNase H catalytic domain D192N mutant in complex with Ca2+ and RNA/DNA hybrid (non-P nick at the active site) | ||||||
Components |
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Keywords | HYDROLASE/RNA/DNA / RNase H / Ribonuclease H / RNA/DNA hybrid / HYDROLASE-RNA-DNA COMPLEX | ||||||
Function / homology | Function and homology information ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Nowotny, M. / Yang, W. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. Authors: Nowotny, M. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g8k.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g8k.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 2g8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/2g8k ftp://data.pdbj.org/pub/pdb/validation_reports/g8/2g8k | HTTPS FTP |
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-Related structure data
Related structure data | 2g8fC 2g8hC 2g8iC 2g8uC 2g8vC 2g8wC 1zbiS 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
#1: RNA chain | Mass: 1875.189 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 1824.228 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 16329.476 Da / Num. of mol.: 1 / Fragment: Bh-RNase HC / Mutation: D192N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: rnhA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q9KEI9, ribonuclease H | ||
#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: 2.32 Å3/Da / Density % sol: 46.92 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 27% MPD, 0.25M ammonium acetate, Na Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 278K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 22448 / Num. obs: 20635 / % possible obs: 91.9 % / Observed criterion σ(I): 3.2 |
Reflection shell | Resolution: 1.65→1.71 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZBI Resolution: 1.65→30 Å / σ(F): 3.2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.65→30 Å
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Refine LS restraints |
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