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Yorodumi- PDB-6qy6: Crystal structure of the CCA-adding enzyme of a psychrophilic organism -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qy6 | |||||||||
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Title | Crystal structure of the CCA-adding enzyme of a psychrophilic organism | |||||||||
Components | CCA-adding enzymeCCA tRNA nucleotidyltransferase | |||||||||
Keywords | RNA BINDING PROTEIN / tRNA maturation / tRNA nucleotidyltransferase / psychrophilic enzyme | |||||||||
Function / homology | Function and homology information RNA 3'-end processing / tRNA processing / nucleotidyltransferase activity / nucleotide binding / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Planococcus halocryophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | de Wijn, R. / Rollet, K. / Bluhm, A. / Hennig, O. / Betat, H. / Moerl, M. / Lorber, B. / Sauter, C. | |||||||||
Funding support | France, 2items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2021 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. / Wellner, K. / Betat, H. / Morl, M. / Sauter, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qy6.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qy6.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 6qy6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/6qy6 ftp://data.pdbj.org/pub/pdb/validation_reports/qy/6qy6 | HTTPS FTP |
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-Related structure data
Related structure data | 6qxnC 1mivS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Planococcus halocryophilus (bacteria) / Gene: BBI08_05760 / Plasmid: pET-30(+) / Details (production host): pET-30 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A1C7DQ98, CCA tRNA nucleotidyltransferase | ||||
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#2: Chemical | ChemComp-PO4 / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 65.98 % / Description: bipyramid |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 100 mM Sodium acetate; pH 4.5 1 M di-Ammonium hydrogen phosphate PH range: 4.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 68555 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 44.8 Å2 / CC1/2: 1 / Rrim(I) all: 0.074 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 0.66 / Num. unique obs: 10787 / CC1/2: 0.59 / Rrim(I) all: 2.648 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MIV Resolution: 1.8→39.926 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→39.926 Å
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Refine LS restraints |
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LS refinement shell |
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