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- PDB-6n67: Crystal structure of the ligase domain of fungal tRNA ligase Trl1 -

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Basic information

Entry
Database: PDB / ID: 6n67
TitleCrystal structure of the ligase domain of fungal tRNA ligase Trl1
ComponentstRNA ligase
KeywordsLIGASE / RNA ligase / tRNA splicing / inhibitor / ATP-binding
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 / tRNA ligase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPeschek, J. / Walter, P.
CitationJournal: Elife / Year: 2019
Title: tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay.
Authors: Peschek, J. / Walter, P.
History
DepositionNov 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,23411
Polymers49,0611
Non-polymers1,17210
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-51 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.729, 56.580, 173.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein tRNA ligase


Mass: 49061.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0034810 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: G0S6G2, RNA ligase (ATP)

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Non-polymers , 5 types, 286 molecules

#2: 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 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: ammonium sulfate, sodium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→37.74 Å / Num. obs: 39302 / % possible obs: 99.3 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.036 / Rrim(I) all: 0.073 / Net I/σ(I): 10.3 / Num. measured all: 159936 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.944.11.02924950.7930.5751.18499.1
9.11-37.743.70.0274360.9980.0150.03298.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
Aimless0.5.27data scaling
CRANK2phasing
Cootmodel building
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.9→37.74 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.756 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.126
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1924 4.9 %RANDOM
Rwork0.1695 ---
obs0.1717 37320 98.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 144.96 Å2 / Biso mean: 47.465 Å2 / Biso min: 25.53 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å2-0 Å20 Å2
2--0.76 Å2-0 Å2
3----3.78 Å2
Refinement stepCycle: final / Resolution: 1.9→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 68 276 3457
Biso mean--55.85 51.63 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133244
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172989
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.6574380
X-RAY DIFFRACTIONr_angle_other_deg1.2671.5886941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0215385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.98521.921177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16715555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5951523
X-RAY DIFFRACTIONr_chiral_restr0.0660.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02698
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 129 -
Rwork0.343 2709 -
all-2838 -
obs--98.3 %
Refinement TLS params.Method: refined / Origin x: 34.0167 Å / Origin y: 5.8281 Å / Origin z: 23.8975 Å
111213212223313233
T0.0296 Å20.0162 Å20.0068 Å2-0.0426 Å2-0.0195 Å2--0.0207 Å2
L0.1395 °20.151 °2-0.1426 °2-0.2939 °2-0.3941 °2--1.0592 °2
S0.0222 Å °0.0378 Å °-0.0299 Å °0.0377 Å °-0.0141 Å °0.0069 Å °0.0599 Å °0.1267 Å °-0.0081 Å °

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