+Open data
-Basic information
Entry | Database: PDB / ID: 8ucf | ||||||
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Title | Thermophilic RNA Ligase from Palaeococcus pacificus K238G | ||||||
Components | ATP dependent DNA ligase | ||||||
Keywords | LIGASE / RNA ligase / thermophilic / Archaea / Rnl3 / nucleotidyl-transferase | ||||||
Function / homology | RNA ligase, Pab1020 family / RNA ligase Pab1020, C-terminal domain / Ligase Pab1020 C-terminal region / RNA ligase domain, REL/Rln2 / RNA ligase / ligase activity / ATP dependent DNA ligase Function and homology information | ||||||
Biological species | Palaeococcus pacificus DY20341 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rousseau, M.D. / Hicks, J.L. / Oulavallickal, T. / Williamson, A. / Arcus, V.L. / Patrick, M.W. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus. Authors: Rousseau, M. / Oulavallickal, T. / Williamson, A. / Arcus, V. / Patrick, W.M. / Hicks, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ucf.cif.gz | 210.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ucf.ent.gz | 138.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ucf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ucf_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8ucf_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8ucf_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 8ucf_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/8ucf ftp://data.pdbj.org/pub/pdb/validation_reports/uc/8ucf | HTTPS FTP |
-Related structure data
Related structure data | 8uceC 8ucgC 8uchC 8uciC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 46902.000 Da / Num. of mol.: 1 / Mutation: K238G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Palaeococcus pacificus DY20341 (archaea) Gene: PAP_02190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A075LQ94, RNA ligase (ATP) | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.31 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 80 mM potassium chloride, 20 mM magnesium chloride hexahydrate, 40 mM sodium cacodylate trihydrate pH 6.5, 40% v/v (+/-)-2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.57 Å / Num. obs: 44026 / % possible obs: 99.96 % / Redundancy: 13.7 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.07396 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.9→1.926 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.06594 / Mean I/σ(I) obs: 4.73 / Num. unique obs: 9589 / % possible all: 99.89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.57 Å / SU ML: 0.1683 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.779 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.57 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -16.9275051648 Å / Origin y: -27.8222783734 Å / Origin z: 21.7696544982 Å
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Refinement TLS group | Selection details: all |