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- PDB-9r3w: Fungal tRNA ligase Trl1-LIG-KIN -

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Basic information

Entry
Database: PDB / ID: 9r3w
TitleFungal tRNA ligase Trl1-LIG-KIN
ComponentstRNA ligase
KeywordsLIGASE / tRNA ligase / polynucleotide kinase / tRNA splicing / adenylyltransferase
Function / homology
Function and homology information


GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / RNA ligase (ATP) / RNA ligase (ATP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / phosphoric diester hydrolase activity / ATP binding / metal ion binding / nucleus
Similarity search - Function
tRNA ligase Trl1, fungi / tRNA ligase, phosphodiesterase / tRNA ligase, kinase domain, fungi / Fungal tRNA ligase phosphodiesterase domain / tRNA ligase kinase domain / T4 RNA ligase 1, N-terminal / RNA ligase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / GUANOSINE-5'-DIPHOSPHATE / tRNA ligase
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsPeschek, J. / Koehler, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)442512666 Germany
German Research Foundation (DFG)439669440 Germany
CitationJournal: Rna / Year: 2025
Title: Interdomain assembly between the fungal tRNA ligase adenylyltransferase and kinase domain.
Authors: Kohler, S. / Peschek, J.
History
DepositionMay 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9535
Polymers70,8121
Non-polymers1,1414
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-35 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.674, 112.674, 108.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-818-

HOH

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Components

#1: Protein tRNA ligase


Mass: 70811.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal 6xHis tag was proteolytically removed prior to crystallization
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0034810 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S6G2, RNA ligase (ATP)
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 41%(v/v) PEG 400 and 0.1 M imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 5, 2024 / Details: Vertical CRL / Horizontal Elliptical mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.89→48.8 Å / Num. obs: 1492263 / % possible obs: 100 % / Redundancy: 26.5 % / Biso Wilson estimate: 37.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.033 / Rrim(I) all: 0.171 / Net I/σ(I): 17.7
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 26.6 % / Rmerge(I) obs: 2.801 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 144695 / CC1/2: 0.612 / Rpim(I) all: 0.551 / Rrim(I) all: 2.855 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSVERSION Jun 30, 2023 BUILT=20230630data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→48.8 Å / SU ML: 0.2233 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 5303 4.97 %Random selection
Rwork0.1816 101341 --
obs0.1835 106644 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.19 Å2
Refinement stepCycle: LAST / Resolution: 1.89→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 69 348 5277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01145036
X-RAY DIFFRACTIONf_angle_d1.14636826
X-RAY DIFFRACTIONf_chiral_restr0.0677739
X-RAY DIFFRACTIONf_plane_restr0.0133881
X-RAY DIFFRACTIONf_dihedral_angle_d10.8836683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.910.38091550.34063411X-RAY DIFFRACTION100
1.91-1.930.3391560.30363378X-RAY DIFFRACTION99.94
1.93-1.960.32651940.29263369X-RAY DIFFRACTION99.94
1.96-1.980.3421570.26293386X-RAY DIFFRACTION100
1.98-2.010.34641540.25883399X-RAY DIFFRACTION100
2.01-2.040.27691900.24963353X-RAY DIFFRACTION100
2.04-2.070.23181710.23993412X-RAY DIFFRACTION99.94
2.07-2.10.25111790.22953351X-RAY DIFFRACTION100
2.1-2.130.23541620.22453394X-RAY DIFFRACTION100
2.13-2.160.24231840.20443388X-RAY DIFFRACTION100
2.16-2.20.23411950.19153346X-RAY DIFFRACTION100
2.2-2.240.20391780.1953375X-RAY DIFFRACTION100
2.24-2.280.24581930.19613354X-RAY DIFFRACTION100
2.28-2.330.23571930.18933358X-RAY DIFFRACTION100
2.33-2.380.23921710.17783383X-RAY DIFFRACTION100
2.38-2.440.21691550.19243387X-RAY DIFFRACTION100
2.44-2.50.22431760.19053419X-RAY DIFFRACTION100
2.5-2.570.25231750.193367X-RAY DIFFRACTION100
2.57-2.640.23331590.18913400X-RAY DIFFRACTION100
2.64-2.730.24981800.19693358X-RAY DIFFRACTION100
2.73-2.820.22821810.19293373X-RAY DIFFRACTION100
2.82-2.940.25721980.20133372X-RAY DIFFRACTION100
2.94-3.070.23791760.19213385X-RAY DIFFRACTION100
3.07-3.230.2581630.1893382X-RAY DIFFRACTION100
3.23-3.430.22811560.18643402X-RAY DIFFRACTION100
3.43-3.70.21681930.1643373X-RAY DIFFRACTION100
3.7-4.070.18431890.14963350X-RAY DIFFRACTION100
4.07-4.660.15012150.14633336X-RAY DIFFRACTION100
4.66-5.870.241530.15743409X-RAY DIFFRACTION100
5.87-48.80.18872020.1693371X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: 24.7394646176 Å / Origin y: -12.484711649 Å / Origin z: 27.0110502706 Å
111213212223313233
T0.25266651821 Å20.00668528668212 Å20.010829448402 Å2-0.286580106808 Å2-0.0264117691924 Å2--0.280168552171 Å2
L0.456253546556 °20.286795994932 °2-0.0447778863151 °2-0.784292852298 °2-0.134009070189 °2--0.392865986939 °2
S-0.00474242297539 Å °0.00558788945938 Å °0.033371227092 Å °-0.0402454313028 Å °0.00488829431718 Å °0.0039601503064 Å °0.0462368115413 Å °-0.0284235708937 Å °-0.00152983966159 Å °
Refinement TLS groupSelection details: all

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