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- PDB-8uce: Thermophilic RNA Ligase from Palaeococcus pacificus + AMP -

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Basic information

Entry
Database: PDB / ID: 8uce
TitleThermophilic RNA Ligase from Palaeococcus pacificus + AMP
ComponentsATP dependent DNA ligase
KeywordsLIGASE / RNA ligase / thermophilic / Archaea / Rnl3 / nucleotidyl-transferase
Function / homology
Function and homology information


ligase activity / ATP binding / metal ion binding
Similarity search - Function
RNA ligase, Pab1020 family / RNA ligase Pab1020, C-terminal domain / Ligase Pab1020 C-terminal region / RNA ligase domain, REL/Rln2 / RNA ligase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ATP dependent DNA ligase
Similarity search - Component
Biological speciesPalaeococcus pacificus DY20341 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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)95,38515
Polymers93,9482
Non-polymers1,43613
Water8,575476
1
A: ATP dependent DNA ligase
hetero molecules

B: ATP dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,38515
Polymers93,9482
Non-polymers1,43613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area7710 Å2
ΔGint-79 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.216, 98.799, 142.977
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 and (name N or name...
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 - 1522 - 36
d_12GLUGLUVALVALAA17 - 38038 - 401
d_13AMPAMPAMPAMPAC401
d_14GOLGOLGOLGOLAD402
d_15GOLGOLGOLGOLAE403
d_21METMETVALVALBB1 - 38022 - 401
d_22AMPAMPAMPAMPBK401
d_23GOLGOLGOLGOLBL402
d_24GOLGOLGOLGOLBM403

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), (-0.00389180409775, 0.999976781262, -0.00559381775697), (-0.00134701748658, 0.00558861275899, 0.999983476339)
Vector: 40.3995719944, 49.6300839207, 4.07916800521)

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Components

#1: Protein ATP dependent DNA ligase


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 ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 476 / 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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 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

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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: May 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
Zanudav7.1data reduction
XDSv7.1data scaling
PHENIX1.19.2_4158phasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.237 1838 3.02 %
Rwork0.1894 58956 -
obs0.1908 60794 92.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.31 Å2
Refinement stepCycle: LAST / Resolution: 2.12→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 0 90 476 6571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00786226
X-RAY DIFFRACTIONf_angle_d0.86018403
X-RAY DIFFRACTIONf_chiral_restr0.0541915
X-RAY DIFFRACTIONf_plane_restr0.00751068
X-RAY DIFFRACTIONf_dihedral_angle_d11.8207869
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.04297202408 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.180.32581250.27523994X-RAY DIFFRACTION82.25
2.18-2.240.27411300.244119X-RAY DIFFRACTION84.59
2.24-2.310.25071300.21464193X-RAY DIFFRACTION86.36
2.31-2.40.26761370.19894323X-RAY DIFFRACTION89.08
2.4-2.490.22311330.19514333X-RAY DIFFRACTION89.04
2.49-2.610.23831440.20224428X-RAY DIFFRACTION90.36
2.61-2.740.23871360.18814517X-RAY DIFFRACTION92.62
2.74-2.910.25071410.18654615X-RAY DIFFRACTION94.35
2.92-3.140.24671480.18214689X-RAY DIFFRACTION95.56
3.14-3.460.22571470.17754796X-RAY DIFFRACTION97.34
3.46-3.960.20541530.16164895X-RAY DIFFRACTION98.56
3.96-4.980.2081530.15414950X-RAY DIFFRACTION98.99
4.98-42.930.24731610.21395104X-RAY DIFFRACTION98.03
Refinement TLS params.Method: refined / Origin x: 23.8217563143 Å / Origin y: 53.5810252049 Å / Origin z: 49.9829031715 Å
111213212223313233
T0.155848800852 Å20.0343145041804 Å2-0.0133685501449 Å2-0.202988768993 Å20.0329144740021 Å2--0.145682190505 Å2
L0.276146570857 °20.181651801632 °2-0.0203934592012 °2-0.219619791914 °20.027954806083 °2--0.144055952837 °2
S0.017112607087 Å °-0.00756477267769 Å °0.0433658948319 Å °0.021166345086 Å °-0.00376312270504 Å °0.0453646932067 Å °-0.0187652640197 Å °-0.0586562059818 Å °-0.0114061719457 Å °
Refinement TLS groupSelection details: all

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