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- PDB-8uch: Thermophilic RNA Ligase from Palaeococcus pacificus K92A + ATP -

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Basic information

Entry
Database: PDB / ID: 8uch
TitleThermophilic RNA Ligase from Palaeococcus pacificus K92A + ATP
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 / ADENOSINE-5'-TRIPHOSPHATE / SPERMIDINE / ATP dependent DNA ligase
Function and homology information
Biological speciesPalaeococcus pacificus DY20341 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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)48,07913
Polymers46,9161
Non-polymers1,16312
Water3,819212
1
A: ATP dependent DNA ligase
hetero molecules

A: ATP dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,15726
Polymers93,8322
Non-polymers2,32524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9510 Å2
ΔGint-161 kcal/mol
Surface area31550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.020, 97.251, 140.101
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-703-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ATP dependent DNA ligase


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 / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.69 %
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 7.0, 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: 0.953659 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953659 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.217→46.72 Å / Rmerge(I) obs: 0.9675 / Mean I/σ(I) obs: 2.55 / Num. unique obs: 3098

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Zanudav7.1data reduction
XDSv7.1data scaling
PHENIX1.20.1_4487phasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2046 2000 6.4 %
Rwork0.1699 29262 -
obs0.1721 31262 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.55 Å2
Refinement stepCycle: LAST / Resolution: 2.14→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 71 212 3276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673134
X-RAY DIFFRACTIONf_angle_d0.78494234
X-RAY DIFFRACTIONf_chiral_restr0.0546459
X-RAY DIFFRACTIONf_plane_restr0.0083537
X-RAY DIFFRACTIONf_dihedral_angle_d9.0631440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.190.26161430.21132085X-RAY DIFFRACTION99.96
2.19-2.250.23461380.20122031X-RAY DIFFRACTION100
2.25-2.320.25951430.18252084X-RAY DIFFRACTION100
2.32-2.390.23561400.19082048X-RAY DIFFRACTION100
2.39-2.480.25331410.18562078X-RAY DIFFRACTION100
2.48-2.580.21841420.17822068X-RAY DIFFRACTION100
2.58-2.70.18241420.16362080X-RAY DIFFRACTION100
2.7-2.840.21371410.16072055X-RAY DIFFRACTION100
2.84-3.020.20691430.15582101X-RAY DIFFRACTION100
3.02-3.250.18251430.15452080X-RAY DIFFRACTION100
3.25-3.580.1831440.14632108X-RAY DIFFRACTION99.96
3.58-4.090.19011420.14882094X-RAY DIFFRACTION99.96
4.09-5.150.16261470.14642135X-RAY DIFFRACTION100
5.16-46.720.21981510.21272215X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 57.7905638155 Å / Origin y: 20.7023073719 Å / Origin z: 48.3891654255 Å
111213212223313233
T0.0808859817361 Å20.0127667807339 Å2-0.00852487437825 Å2-0.167707130047 Å2-0.0455255987756 Å2--0.15896113505 Å2
L1.04733362706 °2-0.191727234284 °20.399200240257 °2-0.477280801417 °2-0.384825464639 °2--0.897556907636 °2
S0.0212759800516 Å °-0.0112308978168 Å °-0.0487981115499 Å °0.0170207407639 Å °0.0339072298526 Å °-0.0590780982646 Å °0.0501856127009 Å °0.149835125042 Å °-0.0509788331361 Å °
Refinement TLS groupSelection details: all

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