+Open data
-Basic information
Entry | Database: PDB / ID: 2d0a | ||||||
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Title | Crystal structure of Bst-RNase HIII | ||||||
Components | ribonuclease HIII | ||||||
Keywords | HYDROLASE / Ribonuclease H / RNA/DNA hybrid | ||||||
Function / homology | Function and homology information RNA catabolic process / ribonuclease H / RNA-DNA hybrid ribonuclease activity / magnesium ion binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å | ||||||
Authors | Chon, H. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal structure and structure-based mutational analyses of RNase HIII from Bacillus stearothermophilus: a new type 2 RNase H with TBP-like substrate-binding domain at the N terminus Authors: Chon, H. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d0a.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d0a.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 2d0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/2d0a ftp://data.pdbj.org/pub/pdb/validation_reports/d0/2d0a | HTTPS FTP |
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-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: 33872.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): MIC2067(DE3) / References: UniProt: Q6L6Q4, ribonuclease H |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.39 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.0066 Å |
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Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jul 2, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0066 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 15163 / Biso Wilson estimate: 26.1 Å2 |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MIR / Resolution: 2.3→19.44 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1354273.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.5448 Å2 / ksol: 0.32578 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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