+Open data
-Basic information
Entry | Database: PDB / ID: 8uce | ||||||
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Title | Thermophilic RNA Ligase from Palaeococcus pacificus + AMP | ||||||
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 / ADENOSINE MONOPHOSPHATE / ATP dependent DNA ligase Function and homology information | ||||||
Biological species | Palaeococcus pacificus DY20341 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 | 8uce.cif.gz | 399.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uce.ent.gz | 267.2 KB | Display | PDB format |
PDBx/mmJSON format | 8uce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uce_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 8uce_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 8uce_validation.xml.gz | 33.5 KB | Display | |
Data in CIF | 8uce_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/8uce ftp://data.pdbj.org/pub/pdb/validation_reports/uc/8uce | HTTPS FTP |
-Related structure data
Related structure data | 8ucfC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (0.999991519666, 0.00389927476123, 0.0013252364245), (-0.00389180409775, 0.999976781262, -0.00559381775697), (-0.00134701748658, 0.00558861275899, 0.999983476339)Vector: ...NCS oper: (Code: given Matrix: (0.999991519666, 0.00389927476123, 0.0013252364245), Vector: |
-Components
#1: Protein | Mass: 46974.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Palaeococcus pacificus DY20341 (archaea) Gene: PAP_02190 / Plasmid: PET28b / Details (production host): Kanamycin Resistance / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A075LQ94 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | 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: 3.05 Å3/Da / Density % sol: 59.71 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 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: 0.953725 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953725 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→42.93 Å / Num. obs: 65953 / % possible obs: 93.2 % / Redundancy: 13.6 % / Biso Wilson estimate: 21.18 Å2 / Rmerge(I) obs: 0.1462 / Net I/σ(I): 14.53 |
Reflection shell | Resolution: 2.15→47.66 Å / Redundancy: 13 % / Rmerge(I) obs: 1.275 / Mean I/σ(I) obs: 3.36 / Num. unique obs: 6536 / % possible all: 84.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→42.93 Å / SU ML: 0.2444 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 26.8067 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: 27.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→42.93 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 2.04297202408 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 23.8217563143 Å / Origin y: 53.5810252049 Å / Origin z: 49.9829031715 Å
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Refinement TLS group | Selection details: all |