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Yorodumi- PDB-1io2: Crystal structure of type 2 ribonuclease h from hyperthermophilic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1io2 | ||||||
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Title | Crystal structure of type 2 ribonuclease h from hyperthermophilic archaeon, thermococcus kodakaraensis kod1 | ||||||
Components | RIBONUCLEASE HII | ||||||
Keywords | HYDROLASE / endonuclease | ||||||
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 | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Muroya, A. / Tsuchiya, D. / Ishikawa, M. / Haruki, M. / Morikawa, M. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses. Authors: Muroya, A. / Tsuchiya, D. / Ishikawa, M. / Haruki, M. / Morikawa, M. / Kanaya, S. / Morikawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1io2.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1io2.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 1io2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/1io2 ftp://data.pdbj.org/pub/pdb/validation_reports/io/1io2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23974.449 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: RNHB / Plasmid: PJAL700K / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: O74035, ribonuclease H |
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#2: 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: 2.59 Å3/Da / Density % sol: 52.59 % | |||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 6000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 19, 1999 / Details: MONOCHROMETER |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 52662 / Num. obs: 15205 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 4.6 / % possible all: 73.7 |
Reflection shell | *PLUS % possible obs: 73.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→15 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.4 Å2 / ksol: 0.435 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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