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Open data
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Basic information
Entry | Database: PDB / ID: 8uce | ||||||
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Title | Thermophilic RNA Ligase from Palaeococcus pacificus + AMP | ||||||
![]() | ATP dependent DNA ligase | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rousseau, M.D. / Hicks, J.L. / Oulavallickal, T. / Williamson, A. / Arcus, V.L. / Patrick, M.W. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 399.5 KB | Display | ![]() |
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PDB format | ![]() | 267.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 33.5 KB | Display | |
Data in CIF | ![]() | 49 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ucfC ![]() 8ucgC ![]() 8uchC ![]() 8uciC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: |
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Components
#1: Protein | Mass: 46974.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PAP_02190 / Plasmid: PET28b / Details (production host): Kanamycin Resistance / Production host: ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |