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Open data
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Basic information
Entry | Database: PDB / ID: 3bk2 | ||||||
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Title | Crystal Structure Analysis of the RNase J/UMP complex | ||||||
![]() | Metal dependent hydrolase | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() 5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | de la Sierra-Gallay, I.L. / Zig, L. / Putzer, H. | ||||||
![]() | ![]() Title: Structural insights into the dual activity of RNase J Authors: de la Sierra-Gallay, I.L. / Zig, L. / Jamalli, A. / Putzer, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.4 KB | Display | ![]() |
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PDB format | ![]() | 98.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 589.7 KB | Display | ![]() |
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Full document | ![]() | 601.8 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bk1SC S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63305.957 Da / Num. of mol.: 1 / Fragment: UNP residues 20-573 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 182 molecules 








#2: Chemical | ChemComp-SO4 / ![]() | ||||||
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#3: Chemical | #4: Chemical | ChemComp-U5P / | ![]() #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.85 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2-4% PEG 4K, 0.02M ammonium sulfate, 0.1M Na-MES, The RNase J/UMP complex was obtained by soaking of a native RNase J crystal in 100mM UMP, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→50 Å / Num. all: 38744 / Num. obs: 38615 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.97 / Num. unique all: 4991 / % possible all: 94.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3BK1 Resolution: 2.1→50 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 55.659 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.961 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014
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Xplor file |
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