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Open data
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Basic information
Entry | Database: PDB / ID: 6z2b | ||||||
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Title | Toprim domain of RNase M5 bound with two Mg2+ ions | ||||||
![]() | Ribonuclease M5 | ||||||
![]() | HYDROLASE / Toprim domain / ribonuclease / magnesium binding / RNase M5 / ribosomal RNA ribonuclease | ||||||
Function / homology | ![]() ribonuclease M5 / ribonuclease M5 activity / rRNA processing / rRNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oerum, S. / Catala, M. / Tisne, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural studies of RNase M5 reveal two-metal-ion supported two-step dsRNA cleavage for 5S rRNA maturation. Authors: Oerum, S. / Catala, M. / Bourguet, M. / Gilet, L. / Barraud, P. / Cianferani, S. / Condon, C. / Tisne, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.7 KB | Display | ![]() |
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PDB format | ![]() | 142.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 687.8 KB | Display | ![]() |
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Full document | ![]() | 693.5 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tg6S 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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Unit cell |
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Components
#1: Protein | Mass: 12528.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rnmV, B4109_0079, B4114_0027, D9548_05595, TGS27_1231 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate trihydrate pH 4.6, 30% (w/v) polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.138→43.675 Å / Num. obs: 23254 / % possible obs: 99.66 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 11.99 |
Reflection shell | Resolution: 2.14→2.22 Å / Num. unique obs: 2238 / CC1/2: 0.633 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6TG6 Resolution: 2.138→43.675 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.88 Å2 / Biso mean: 64.163 Å2 / Biso min: 30.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.138→43.675 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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