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- PDB-1i3a: RNASE HII FROM ARCHAEOGLOBUS FULGIDUS WITH COBALT HEXAMMINE CHLORIDE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1i3a | ||||||
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Title | RNASE HII FROM ARCHAEOGLOBUS FULGIDUS WITH COBALT HEXAMMINE CHLORIDE | ||||||
![]() | RIBONUCLEASE HII | ||||||
![]() | HYDROLASE / mixed beta sheet / helix-loop-helix | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chapados, B.R. / Chai, Q. / Hosfield, D.J. / Qiu, J. / Shen, B. / Tainer, J.A. | ||||||
![]() | ![]() Title: Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication. Authors: Chapados, B.R. / Chai, Q. / Hosfield, D.J. / Qiu, J. / Shen, B. / Tainer, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.5 KB | Display | ![]() |
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PDB format | ![]() | 39.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442 KB | Display | ![]() |
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Full document | ![]() | 444.8 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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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Details | The biologically relevent molecule is a monomer in the asymmetric unit |
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Components
#1: Protein | Mass: 25393.240 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NCO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.24 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10% MPEG 5000, 10% butanol, 20 mM sodium citrate, 100 mM Tris pH 8.5, (soak: 10mM Co(III)(NH2)6), VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal amounts of protein and precipitant solutions | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 94 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2000 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.863 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→35 Å / Num. all: 13210 / Num. obs: 13210 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.414 / % possible all: 93.3 |
Reflection | *PLUS Num. measured all: 82747 |
Reflection shell | *PLUS % possible obs: 93.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ARNASE HII refined model (rcsb012848) Resolution: 2.15→19.75 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: NULL
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Refinement step | Cycle: LAST / Resolution: 2.15→19.75 Å
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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