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- PDB-4ojm: Crystal structure of a C-terminally truncated CYT-18 protein incl... -

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Basic information

Entry
Database: PDB / ID: 4ojm
TitleCrystal structure of a C-terminally truncated CYT-18 protein including N-terminal residues
ComponentsTyrosine--tRNA ligase, mitochondrial
KeywordsLIGASE / TyrRS / tRNA ligase / splicing
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. / Geng, C.
CitationJournal: Biochemistry / Year: 2014
Title: An in Vitro Peptide Complementation Assay for CYT-18-Dependent Group I Intron Splicing Reveals a New Role for the N-Terminus.
Authors: Geng, C. / Paukstelis, P.J.
History
DepositionJan 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Tyrosine--tRNA ligase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1032
Polymers44,9221
Non-polymers1811
Water5,801322
1
X: Tyrosine--tRNA ligase, mitochondrial
hetero molecules

X: Tyrosine--tRNA ligase, 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 area2980 Å2
ΔGint-30 kcal/mol
Surface area33590 Å2
MethodPISA
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-907-

HOH

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Components

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


Mass: 44922.129 Da / Num. of mol.: 1 / Fragment: UNP residues 33-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 / OR74A
Gene: cyt-18, B18P24.070, NCU03030 / References: UniProt: P12063, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYR / TYROSINE


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


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.58 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / 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→58.58 Å / Num. all: 25832 / Num. obs: 25832 / % possible obs: 94.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y42

1y42


Resolution: 1.95→58.58 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.226 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21125 1936 7 %RANDOM
Rwork0.16727 ---
obs0.17081 25832 94.87 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å20.43 Å2
2---1.53 Å2-0 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.95→58.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3071 0 13 322 3406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193177
X-RAY DIFFRACTIONr_bond_other_d0.0010.023002
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9434290
X-RAY DIFFRACTIONr_angle_other_deg0.73636914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4555385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0823.791153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53215567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6731522
X-RAY DIFFRACTIONr_chiral_restr0.0690.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213585
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02757
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.332.1041535
X-RAY DIFFRACTIONr_mcbond_other2.3212.1021534
X-RAY DIFFRACTIONr_mcangle_it3.543.1251914
X-RAY DIFFRACTIONr_mcangle_other3.5453.1271915
X-RAY DIFFRACTIONr_scbond_it2.6952.3731642
X-RAY DIFFRACTIONr_scbond_other2.6942.3721642
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2633.4272374
X-RAY DIFFRACTIONr_long_range_B_refined7.09417.5734036
X-RAY DIFFRACTIONr_long_range_B_other7.02917.0973919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 77 -
Rwork0.202 1583 -
obs--76.82 %

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