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- PDB-8ucg: Thermophilic RNA Ligase from Palaeococcus pacificus K92A -

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Basic information

Entry
Database: PDB / ID: 8ucg
TitleThermophilic RNA Ligase from Palaeococcus pacificus K92A
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 binding / metal ion binding / ATP dependent DNA ligase
Function and homology information
Biological speciesPalaeococcus pacificus DY20341 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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

Downloads & links

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Assembly

Deposited unit
A: ATP dependent DNA ligase
B: ATP dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,20912
Polymers93,8322
Non-polymers37710
Water11,836657
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-113 kcal/mol
Surface area31830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.793, 99.699, 142.477
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 3 or (resid 4...
d_2ens_1(chain "B" and (resid 1 through 11 or (resid 12...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETLEULEUAA1 - 1322 - 34
d_12ASPASPGLUGLUAA16 - 9037 - 111
d_13ALAALAPHEPHEAA92 - 264113 - 285
d_14GLNGLNPHEPHEAA266 - 379287 - 400
d_15ASPASPASPASPAA381402
d_21METMETGLUGLUBB1 - 9022 - 111
d_22ALAALAPHEPHEBB92 - 264113 - 285
d_23GLNGLNPHEPHEBB266 - 379287 - 400
d_24ASPASPASPASPBB381402

NCS oper: (Code: givenMatrix: (-0.999969439243, -0.00673916327762, 0.0039628599706), (-0.00661035789565, 0.99947670365, 0.0316642073884), (-0.00417417648408, 0.0316370437835, -0.999490707166)Vector: ...NCS oper: (Code: given
Matrix: (-0.999969439243, -0.00673916327762, 0.0039628599706), (-0.00661035789565, 0.99947670365, 0.0316642073884), (-0.00417417648408, 0.0316370437835, -0.999490707166)
Vector: 121.877681383, -0.869326018213, 75.0170325311)

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Components

#1: Protein ATP dependent DNA ligase


Mass: 46916.027 Da / Num. of mol.: 2 / 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)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 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 6.5, 20% v/v (+/-)-2-methyl-2,4-pentanediol, 12 mM spermine tetrahydrochloride

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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: 0.953725 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 1.86→42.88 Å / Num. obs: 97092 / % possible obs: 99.88 % / Redundancy: 13.8 % / Biso Wilson estimate: 18.56 Å2 / Rmerge(I) obs: 0.07396 / Net I/σ(I): 17.65
Reflection shellResolution: 1.86→1.926 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.8492 / Num. unique obs: 9589 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Zanudav.7.1data reduction
XDSv.7.1data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→42.88 Å / SU ML: 0.2399 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 26.7072
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 4862 5.01 %
Rwork0.2072 92195 -
obs0.2087 97057 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.88 Å2
Refinement stepCycle: LAST / Resolution: 1.86→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 20 657 6665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00586174
X-RAY DIFFRACTIONf_angle_d0.81448345
X-RAY DIFFRACTIONf_chiral_restr0.0577910
X-RAY DIFFRACTIONf_plane_restr0.00641074
X-RAY DIFFRACTIONf_dihedral_angle_d5.0823851
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.642558598116 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.880.39561740.37953034X-RAY DIFFRACTION99.94
1.88-1.90.3471500.33682997X-RAY DIFFRACTION99.78
1.9-1.930.35471580.32033075X-RAY DIFFRACTION99.94
1.93-1.950.34731480.30253022X-RAY DIFFRACTION99.97
1.95-1.980.33441730.28633068X-RAY DIFFRACTION99.82
1.98-20.27621460.27783022X-RAY DIFFRACTION99.81
2-2.030.2881570.24923022X-RAY DIFFRACTION99.81
2.03-2.060.2921450.24113076X-RAY DIFFRACTION99.85
2.06-2.090.26961850.22733018X-RAY DIFFRACTION99.88
2.09-2.130.24411450.21663087X-RAY DIFFRACTION99.91
2.13-2.170.25921670.22313011X-RAY DIFFRACTION99.94
2.17-2.210.24181590.21383044X-RAY DIFFRACTION99.94
2.21-2.250.26291370.21273081X-RAY DIFFRACTION99.75
2.25-2.290.23431720.20223029X-RAY DIFFRACTION99.91
2.29-2.340.25451390.19343074X-RAY DIFFRACTION100
2.34-2.40.25461800.19233049X-RAY DIFFRACTION99.91
2.4-2.460.22571700.19493048X-RAY DIFFRACTION99.88
2.46-2.520.22851510.19593087X-RAY DIFFRACTION99.94
2.52-2.60.26621760.20653054X-RAY DIFFRACTION99.94
2.6-2.680.20261460.20653072X-RAY DIFFRACTION99.97
2.68-2.780.23351740.20833060X-RAY DIFFRACTION99.97
2.78-2.890.24361610.20453071X-RAY DIFFRACTION99.91
2.89-3.020.2521580.19633095X-RAY DIFFRACTION99.91
3.02-3.180.19821630.19443061X-RAY DIFFRACTION99.91
3.18-3.380.20941700.19053108X-RAY DIFFRACTION99.91
3.38-3.640.19631530.16823126X-RAY DIFFRACTION99.94
3.64-4.010.18981720.17173110X-RAY DIFFRACTION100
4.01-4.590.18781740.15213134X-RAY DIFFRACTION99.97
4.59-5.770.21421770.18083158X-RAY DIFFRACTION99.97
5.77-42.880.22091820.21553302X-RAY DIFFRACTION99.49
Refinement TLS params.Method: refined / Origin x: 60.7315288469 Å / Origin y: 70.9662441211 Å / Origin z: 38.4491540426 Å
111213212223313233
T0.114396375107 Å2-0.0137848494925 Å20.0193151927955 Å2-0.0271636298977 Å20.0241863678964 Å2--0.167887172951 Å2
L1.02065571182 °20.0363660797834 °20.47998740014 °2-0.065172965343 °20.0899375305076 °2--1.29708653953 °2
S0.0728781169184 Å °-0.0579405562673 Å °0.00553916887885 Å °0.0114206676493 Å °0.0037527726391 Å °-0.00215812793414 Å °0.0963655006379 Å °-0.0954111874273 Å °-0.0638773691042 Å °
Refinement TLS groupSelection details: all

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