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- PDB-8ucf: Thermophilic RNA Ligase from Palaeococcus pacificus K238G -

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Basic information

Entry
Database: PDB / ID: 8ucf
TitleThermophilic RNA Ligase from Palaeococcus pacificus K238G
ComponentsATP dependent DNA ligase
KeywordsLIGASE / RNA ligase / thermophilic / Archaea / Rnl3 / nucleotidyl-transferase
Function / homologyRNA 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 speciesPalaeococcus pacificus DY20341 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRousseau, M.D. / Hicks, J.L. / Oulavallickal, T. / Williamson, A. / Arcus, V.L. / Patrick, M.W.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Ministry of Business, Innovation and Employment (New Zealand)RTVU1807 New Zealand
CitationJournal: 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
DepositionSep 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5039
Polymers46,9021
Non-polymers6018
Water4,035224
1
A: ATP dependent DNA ligase
hetero molecules

A: ATP dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,00618
Polymers93,8042
Non-polymers1,20216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8120 Å2
ΔGint-80 kcal/mol
Surface area31210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.950, 96.859, 139.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

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Components

#1: Protein ATP dependent DNA ligase


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)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Zanudav7.1data reduction
XDSv7.1data scaling
PHENIX1.19.2_4158phasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1966 2223 5.05 %
Rwork0.1713 41800 -
obs0.1726 44023 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 38 224 3289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713126
X-RAY DIFFRACTIONf_angle_d0.88724214
X-RAY DIFFRACTIONf_chiral_restr0.0602458
X-RAY DIFFRACTIONf_plane_restr0.0152539
X-RAY DIFFRACTIONf_dihedral_angle_d8.0041432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.2611330.21282589X-RAY DIFFRACTION99.63
1.94-1.990.21251330.18192598X-RAY DIFFRACTION100
1.99-2.040.21621330.17162567X-RAY DIFFRACTION100
2.04-2.090.20671480.16372570X-RAY DIFFRACTION100
2.09-2.150.21761360.16482589X-RAY DIFFRACTION100
2.15-2.220.20421640.16052553X-RAY DIFFRACTION100
2.22-2.30.17281470.1592580X-RAY DIFFRACTION100
2.3-2.390.18991230.15862608X-RAY DIFFRACTION100
2.39-2.50.19561280.1692616X-RAY DIFFRACTION100
2.5-2.630.20861530.17012610X-RAY DIFFRACTION100
2.63-2.80.18531230.17182610X-RAY DIFFRACTION100
2.8-3.020.20791280.17112638X-RAY DIFFRACTION100
3.02-3.320.18441510.16912610X-RAY DIFFRACTION100
3.32-3.80.16581420.15972618X-RAY DIFFRACTION100
3.8-4.790.16611240.15762689X-RAY DIFFRACTION100
4.79-46.570.23341570.20532755X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: -16.9275051648 Å / Origin y: -27.8222783734 Å / Origin z: 21.7696544982 Å
111213212223313233
T0.110834887604 Å2-0.0145606357498 Å2-0.00829134062629 Å2-0.095598015702 Å20.0263397752159 Å2--0.126411144854 Å2
L0.800177681888 °20.0665289509729 °20.302240802198 °2-0.440217395325 °20.21209144135 °2--0.77956220233 °2
S0.027462806759 Å °0.0322857395856 Å °-0.0687667021356 Å °-0.0289475940204 Å °0.0297600590335 Å °0.079481483317 Å °0.0811132742543 Å °-0.112244845046 Å °-0.0357296428096 Å °
Refinement TLS groupSelection details: all

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