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Yorodumi- PDB-6q52: Structure of a psychrophilic CCA-adding enzyme in complex with CM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q52 | |||||||||
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Title | Structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP at room temperature in ChipX microfluidic device | |||||||||
Components | CCA-adding enzymeCCA tRNA nucleotidyltransferase | |||||||||
Keywords | RNA BINDING PROTEIN / tRNA maturation / tRNA nucleotidyltransferase / ChipX / 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: 2.3 Å | |||||||||
Authors | de Wijn, R. / Hennig, O. / Rollet, K. / Bluhm, A. / Betat, H. / Moerl, M. / Lorber, B. / Sauter, C. | |||||||||
Funding support | France, 2items
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Citation | Journal: Iucrj / Year: 2019 Title: A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography. Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. ...Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. / Olieric, V. / Gavira, J.A. / Lorber, B. / Sauter, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q52.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q52.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 6q52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/6q52 ftp://data.pdbj.org/pub/pdb/validation_reports/q5/6q52 | HTTPS FTP |
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-Related structure data
Related structure data | 6gzpC 6hw1C 6ibpC 6ibqC 6q3tC 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-30b(+) / Details (production host): pET-30b Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A1C7DQ98, CCA tRNA nucleotidyltransferase |
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#2: Chemical | ChemComp-2TM / |
#3: 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: 3.86 Å3/Da / Density % sol: 68.16 % / Description: bipyramid |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 7.5 Details: protein solution at 5.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 30% (m/v) PEG3350, 200 mM ammonium chloride pH 6.6. Crystallization and crystallographic ...Details: protein solution at 5.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 30% (m/v) PEG3350, 200 mM ammonium chloride pH 6.6. Crystallization and crystallographic analysis were performed using the ChipX microfluidic device. PH range: 6.6-7.5 |
-Data collection
Diffraction | Mean temperature: 293 K / Ambient temp details: in situ / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2016 |
Radiation | Monochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.77 Å / Num. obs: 34862 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 60.56 Å2 / CC1/2: 0.987 / Rrim(I) all: 0.18 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 8.1 % / Num. unique obs: 4066 / CC1/2: 0.469 / Rrim(I) all: 2.312 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MIV Resolution: 2.3→47.77 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.13 Details: triphosphate moiety was modelled in two conformations
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.77 Å
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Refine LS restraints |
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LS refinement shell |
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