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- PDB-8uci: Thermophilic RNA Ligase from Palaeococcus pacificus K238G + AMP -

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Basic information

Entry
Database: PDB / ID: 8uci
TitleThermophilic RNA Ligase from Palaeococcus pacificus K238G + AMP
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 MONOPHOSPHATE / 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
B: ATP dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,70120
Polymers93,8042
Non-polymers1,89718
Water11,079615
1
B: ATP dependent DNA ligase
hetero molecules

A: ATP dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,70120
Polymers93,8042
Non-polymers1,89718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area9050 Å2
ΔGint-86 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.849, 99.722, 143.073
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 and (name N or name...

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_11METMETVALVALAA1 - 38022 - 401
d_12GOLGOLGOLGOLAD402
d_13GOLGOLGOLGOLAE403
d_14GOLGOLGOLGOLAF404
d_15GOLGOLGOLGOLAG405
d_16GOLGOLGOLGOLAH406
d_21METMETVALVALBB1 - 38022 - 401
d_22GOLGOLGOLGOLBM403
d_23GOLGOLGOLGOLBN404
d_24GOLGOLGOLGOLBO405
d_25GOLGOLGOLGOLBP406
d_26GOLGOLGOLGOLBQ407

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Components

#1: Protein ATP dependent DNA ligase


Mass: 46902.000 Da / Num. of mol.: 2 / Mutation: K238G
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, RNA ligase (ATP)
#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.: 12 / 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.: 615 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM potassium chloride, 50 mM magnesium chloride hexahydrate, 50 mM Tris hydrochloride pH 7.5, 20% w/v polyethylene glycol 4,000

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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: 0.953732 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: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.14→47.08 Å / Num. obs: 64482 / % possible obs: 99.88 % / Redundancy: 13.7 % / Biso Wilson estimate: 14.17 Å2 / Rmerge(I) obs: 0.2477 / Net I/σ(I): 11.12
Reflection shellResolution: 2.216→47.08 Å / Redundancy: 14 % / Rmerge(I) obs: 1.325 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 6353 / % possible all: 99.95

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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→47.08 Å / SU ML: 0.2358 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 27.6815
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2399 1999 3.1 %
Rwork0.2056 62442 -
obs0.2067 64441 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.66 Å2
Refinement stepCycle: LAST / Resolution: 2.14→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 120 615 6817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256329
X-RAY DIFFRACTIONf_angle_d0.57328528
X-RAY DIFFRACTIONf_chiral_restr0.0453919
X-RAY DIFFRACTIONf_plane_restr0.00351085
X-RAY DIFFRACTIONf_dihedral_angle_d10.7781885
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.35734544231 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.190.30961400.28124396X-RAY DIFFRACTION99.98
2.19-2.250.33621420.26234412X-RAY DIFFRACTION99.91
2.25-2.320.27211410.24374410X-RAY DIFFRACTION99.93
2.32-2.390.26171410.23754392X-RAY DIFFRACTION99.96
2.39-2.480.25561410.22434407X-RAY DIFFRACTION99.96
2.48-2.580.27081420.22584414X-RAY DIFFRACTION99.91
2.58-2.70.27251420.22214473X-RAY DIFFRACTION99.98
2.7-2.840.24781420.21524409X-RAY DIFFRACTION99.87
2.84-3.020.24621420.20954441X-RAY DIFFRACTION99.87
3.02-3.250.21721420.20534441X-RAY DIFFRACTION99.85
3.25-3.580.25091440.18654491X-RAY DIFFRACTION100
3.58-4.090.2151430.17184489X-RAY DIFFRACTION99.98
4.09-5.160.16381470.15144560X-RAY DIFFRACTION99.92
5.16-47.080.21191500.18784707X-RAY DIFFRACTION99.55
Refinement TLS params.Method: refined / Origin x: 23.7610343132 Å / Origin y: 54.2629242556 Å / Origin z: 49.984284777 Å
111213212223313233
T0.0611533780808 Å20.0270941386899 Å2-0.00813393491917 Å2-0.0670624998039 Å20.0277584406507 Å2--0.0398570745927 Å2
L0.386651189681 °20.121100574899 °2-0.0670071843092 °2-0.1204586329 °20.00360033676319 °2--0.149580398042 °2
S0.024278645256 Å °-0.0245601996418 Å °0.0571887090999 Å °0.0194789989735 Å °-0.0231144221492 Å °0.0326822962125 Å °-0.0302462796355 Å °0.017771134438 Å °-0.00207266957195 Å °
Refinement TLS groupSelection details: all

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