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- PDB-1y42: Crystal structure of a C-terminally truncated CYT-18 protein -

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Basic information

Entry
Database: PDB / ID: 1y42
TitleCrystal structure of a C-terminally truncated CYT-18 protein
ComponentsTyrosyl-tRNA synthetase, mitochondrial
KeywordsLIGASE / CYT-18 / tyrosyl tRNA synthetase / tRNA ligase / group I intron
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Group I intron splicing / RNA folding / positive regulation of RNA splicing / mRNA processing / mitochondrial matrix / mitochondrion ...tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Group I intron splicing / RNA folding / positive regulation of RNA splicing / mRNA processing / mitochondrial matrix / mitochondrion / RNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Tyrosyl-tRNA synthetase, C-terminal / Tyrosyl-tRNA synthetase C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. ...Tyrosyl-tRNA synthetase, C-terminal / Tyrosyl-tRNA synthetase C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / RNA-binding S4 domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TYROSINE / Tyrosine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPaukstelis, P.J. / Coon, R. / Madabusi, L. / Nowakowski, J. / Monzingo, A. / Robertus, J. / Lambowitz, A.M.
CitationJournal: Mol.Cell / Year: 2005
Title: A tyrosyl-tRNA synthetase adapted to function in group I intron splicing by acquiring a new RNA binding surface.
Authors: Paukstelis, P.J. / Coon, R. / Madabusi, L. / Nowakowski, J. / Monzingo, A. / Robertus, J. / Lambowitz, A.M.
History
DepositionNov 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE C-TERMINAL RESIDUES 424-669 WERE DELETED FROM THE SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Tyrosyl-tRNA synthetase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1032
Polymers44,9221
Non-polymers1811
Water3,567198
1
X: Tyrosyl-tRNA synthetase, mitochondrial
hetero molecules

X: Tyrosyl-tRNA synthetase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2074
Polymers89,8442
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2970 Å2
ΔGint-33 kcal/mol
Surface area32340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.880, 73.210, 56.790
Angle α, β, γ (deg.)90.00, 111.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-848-

HOH

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Components

#1: Protein Tyrosyl-tRNA synthetase, mitochondrial / Tyrosine--tRNA ligase / TyrRS


Mass: 44922.129 Da / Num. of mol.: 1 / Fragment: Nucleotide-binding fold, alpha helical domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: cyt-18 / Plasmid: pEX-602 / Production host: Escherichia coli (E. coli) / References: UniProt: P12063, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 28540 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Rsym value: 0.107 / Net I/σ(I): 20.7
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 3 / Num. unique all: 1571 / Rsym value: 0.254 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2TS1

2ts1


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.983 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23541 1936 7 %RANDOM
Rwork0.17395 ---
all0.17886 25832 --
obs0.17886 25832 94.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.176 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å2-0.46 Å2
2--1.48 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 13 198 3161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213036
X-RAY DIFFRACTIONr_bond_other_d0.0020.022700
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9254106
X-RAY DIFFRACTIONr_angle_other_deg0.94736274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2045368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83223.75144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75415519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6831520
X-RAY DIFFRACTIONr_chiral_restr0.1110.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02637
X-RAY DIFFRACTIONr_nbd_refined0.2150.2746
X-RAY DIFFRACTIONr_nbd_other0.2010.22797
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21498
X-RAY DIFFRACTIONr_nbtor_other0.0880.21655
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.050.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.40.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4941.51901
X-RAY DIFFRACTIONr_mcbond_other0.4891.5758
X-RAY DIFFRACTIONr_mcangle_it2.08422951
X-RAY DIFFRACTIONr_scbond_it3.25531342
X-RAY DIFFRACTIONr_scangle_it4.2114.51155
X-RAY DIFFRACTIONr_rigid_bond_restr3.29736504
X-RAY DIFFRACTIONr_sphericity_free9.2443200
X-RAY DIFFRACTIONr_sphericity_bonded2.56135663
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 76 -
Rwork0.167 1571 -
obs--76.71 %

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