+Open data
-Basic information
Entry | Database: PDB / ID: 8uch | ||||||
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Title | Thermophilic RNA Ligase from Palaeococcus pacificus K92A + ATP | ||||||
Components | ATP dependent DNA ligase | ||||||
Keywords | LIGASE / RNA ligase / thermophilic / Archaea / Rnl3 / nucleotidyl-transferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Palaeococcus pacificus DY20341 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 | 8uch.cif.gz | 214.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uch.ent.gz | 139.9 KB | Display | PDB format |
PDBx/mmJSON format | 8uch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uch_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8uch_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8uch_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 8uch_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/8uch ftp://data.pdbj.org/pub/pdb/validation_reports/uc/8uch | HTTPS FTP |
-Related structure data
Related structure data | 8uceC 8ucfC 8ucgC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46916.027 Da / Num. of mol.: 1 / Mutation: K92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Palaeococcus pacificus DY20341 (archaea) Gene: PAP_02190 / Plasmid: PET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A075LQ94, RNA ligase (ATP) |
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-Non-polymers , 6 types, 224 molecules
#2: Chemical | ChemComp-ATP / | ||||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SPD / | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.69 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 80 mM strontium chloride hexahydrate, 20 mM magnesium chloride hexahydrate, 40 mM sodium cacodylate trihydrate pH 7.0, 20% v/v (+/-)-2-methyl-2,4-pentanediol, 12 mM spermine tetrahydrochloride |
-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: 0.953659 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953659 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→46.72 Å / Num. obs: 31266 / % possible obs: 99.97 % / Redundancy: 13.3 % / Biso Wilson estimate: 21.41 Å2 / Rmerge(I) obs: 0.1088 / Net I/σ(I): 16.75 |
Reflection shell | Resolution: 2.217→46.72 Å / Rmerge(I) obs: 0.9675 / Mean I/σ(I) obs: 2.55 / Num. unique obs: 3098 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→46.72 Å / SU ML: 0.1858 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.23 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: 27.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→46.72 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: 57.7905638155 Å / Origin y: 20.7023073719 Å / Origin z: 48.3891654255 Å
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Refinement TLS group | Selection details: all |