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- PDB-3ao9: Crystal structure of the C-terminal domain of sequence-specific r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ao9 | ||||||
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Title | Crystal structure of the C-terminal domain of sequence-specific ribonuclease | ||||||
![]() | Colicin-E5 | ||||||
![]() | HYDROLASE / Ribonuclease | ||||||
Function / homology | ![]() RNA nuclease activity / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Inoue, S. / Fushinobu, S. / Ogawa, T. / Hidaka, M. / Masaki, H. / Yajima, S. | ||||||
![]() | ![]() Title: Identification of the catalytic residues of sequence-specific and histidine-free ribonuclease colicin E5 Authors: Inoue-Ito, S. / Yajima, S. / Fushinobu, S. / Nakamura, S. / Ogawa, T. / Hidaka, M. / Masaki, 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 | ![]() | 52.7 KB | Display | ![]() |
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PDB format | ![]() | 36.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.6 KB | Display | ![]() |
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Full document | ![]() | 437.2 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vj7C ![]() 2djhS 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12854.206 Da / Num. of mol.: 2 / Fragment: C-terminal ribonuclease domain (CRD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P18000, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.57 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50mM MES, 0.1M cadmium chloride, 25% PEG MME, 15% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2006 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 13918 / Num. obs: 13723 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DJH Resolution: 2.1→47.78 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.563 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→47.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.099→2.153 Å / Total num. of bins used: 20
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