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- PDB-1uax: Crystal structure of the ribonuclease H2 from Pyrococcus horikosh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1uax | ||||||
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Title | Crystal structure of the ribonuclease H2 from Pyrococcus horikoshii OT3 | ||||||
![]() | Ribonuclease HII | ||||||
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Function / homology | ![]() RNA catabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hata, T. / Numata, T. / Kakuta, Y. / Kimura, M. | ||||||
![]() | ![]() Title: Crystal structure of the ribonuclease H2 from Pyrococcus horikoshii OT3 Authors: Hata, T. / Numata, T. / Kakuta, Y. / Kimura, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.3 KB | Display | ![]() |
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PDB format | ![]() | 75.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1io2S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25326.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.64 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl, 2M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: OXFORD / Detector: CCD / Date: Feb 1, 2002 / Details: mirrors |
Radiation | Monochromator: Si111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→41.65 Å / Num. all: 55176 / Num. obs: 55176 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.39 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 6.4 / Num. unique all: 2825 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1IO2 Resolution: 2→41.65 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 486885.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.8482 Å2 / ksol: 0.364108 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→41.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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