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- PDB-7otl: Structure of a psychrophilic CCA-adding enzyme crystallized by co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7otl | |||||||||
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Title | Structure of a psychrophilic CCA-adding enzyme crystallized by counter-diffusion | |||||||||
![]() | CCA-adding enzyme | |||||||||
![]() | RNA BINDING PROTEIN / tRNA maturation / tRNA nucleotidyltransferase / psychrophilic enzyme | |||||||||
Function / homology | ![]() tRNA 3'-terminal CCA addition / nucleotidyltransferase activity / tRNA binding / nucleotide binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rollet, K. / de Wijn, R. / Hennig, O. / Betat, H. / Moerl, M. / Lorber, B. / Sauter, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus . Authors: de Wijn, R. / Rollet, K. / Ernst, F.G.M. / Wellner, K. / Betat, H. / Morl, M. / Sauter, 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 | ![]() | 166 KB | Display | ![]() |
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PDB format | ![]() | 124.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.4 KB | Display | ![]() |
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Full document | ![]() | 436.9 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oqxC ![]() 7otrC ![]() 6qxnS 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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Unit cell |
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Components
#1: Protein | Mass: 48498.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.72 % / Description: bipyramid |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 5 Details: Protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; Crystals were obtained in capillaries filled with protein solution and sealed at one extremity and plunged in ...Details: Protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; Crystals were obtained in capillaries filled with protein solution and sealed at one extremity and plunged in 3 M ammonium sulfate, 0.1 M sodium acetate pH 5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 18615 / % possible obs: 98.6 % / Redundancy: 55.7 % / Biso Wilson estimate: 60.29 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.258 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 57.5 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1819 / CC1/2: 1 / Rrim(I) all: 2.04 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QXN Resolution: 2.8→46.88 Å / SU ML: 0.3942 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3979 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 53.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→46.88 Å
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Refine LS restraints |
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LS refinement shell |
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