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- PDB-5ihx: Crystal Structure of a C-terminally truncated Aspergillus nidulan... -

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Basic information

Entry
Database: PDB / ID: 5ihx
TitleCrystal Structure of a C-terminally truncated Aspergillus nidulans mitochondrial tyrosyl-tRNA synthetase
ComponentsTyrosine--tRNA ligase, mitochondrial
KeywordsLIGASE / tRNA Aminoacylation / ATP-binding / Tyrosine-tRNA ligase / nucleotide-binding motif
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / mitochondrion / RNA binding / ATP 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) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...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) / 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
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.298 Å
AuthorsLamech, L.T. / Lambowitz, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM37951 United States
CitationJournal: To be published
Title: Crystal Structure of a C-terminally truncated Aspergillus nidulans mitochondrial tyrosyl-tRNA synthetase
Authors: Lamech, L.T. / Saoji, M. / Paukstelis, P.J. / Lambowitz, A.M.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Tyrosine--tRNA ligase, mitochondrial
B: Tyrosine--tRNA ligase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7413
Polymers90,5592
Non-polymers1811
Water3,909217
1
A: Tyrosine--tRNA ligase, mitochondrial
hetero molecules

B: Tyrosine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)90,7413
Polymers90,5592
Non-polymers1811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area2430 Å2
ΔGint-30 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.461, 84.950, 164.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 45279.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Strain: R153 / Gene: AN1709.2 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: Q5BCM1, 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.: 217 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe UniProt sequence for this gene (AN1709.2) is a partial sequence. The first 132 residues contain ...The UniProt sequence for this gene (AN1709.2) is a partial sequence. The first 132 residues contain the mitochondrial targeting sequence and one of the conserved motifs of tyrosyl-tRNA synthetases involved in charging tyrosine with AMP. The Aspergillus nidulans mtTyrRS sequence was cloned from a cDNA library which includes the upstream 132 residue sequence. The full-length protein has been characterized in a previous publication: Paukstelis, P. J., and Lambowitz, A. M. (2008) Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity. Proc. Natl. Acad. Sci. U. S. A. 105, 6010-6015.

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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: 2.68 Å3/Da / Density % sol: 54.03 % / Mosaicity: 0.881 °
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.5
Details: 10 mM Tris-HCl pH 8.5, 8% PEG 8000, 1 mM L-tyrosine, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.298→50 Å / Num. obs: 44001 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.46 Å2 / Rmerge(I) obs: 0.112 / Net I/av σ(I): 19.712 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.345.50.7241100
2.34-2.386.10.6591100
2.38-2.436.80.6451100
2.43-2.486.90.5471100
2.48-2.5370.491100
2.53-2.596.90.421100
2.59-2.666.90.3571100
2.66-2.736.90.3221100
2.73-2.816.90.2721100
2.81-2.96.90.2361100
2.9-36.90.1981100
3-3.126.90.1661100
3.12-3.266.90.1411100
3.26-3.446.90.1211100
3.44-3.656.90.1061100
3.65-3.9370.0911100
3.93-4.336.90.0821100
4.33-4.9570.0761100
4.95-6.246.80.0661100
6.24-506.70.0441100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å46.03 Å
Translation3.5 Å46.03 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1535refinement
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.0phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TS1

3ts1


Resolution: 2.298→46.02 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2210 5.04 %Random Selection
Rwork0.1799 ---
obs0.1817 43879 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.298→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 13 217 5643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035563
X-RAY DIFFRACTIONf_angle_d0.727550
X-RAY DIFFRACTIONf_dihedral_angle_d11.5511958
X-RAY DIFFRACTIONf_chiral_restr0.028822
X-RAY DIFFRACTIONf_plane_restr0.003967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2981-2.34810.26291320.21892377X-RAY DIFFRACTION93
2.3481-2.40270.29621260.19632594X-RAY DIFFRACTION100
2.4027-2.46280.241440.1952567X-RAY DIFFRACTION100
2.4628-2.52940.2421400.18682565X-RAY DIFFRACTION100
2.5294-2.60380.23181390.18982592X-RAY DIFFRACTION100
2.6038-2.68780.23681420.18782587X-RAY DIFFRACTION100
2.6878-2.78390.25031440.18912588X-RAY DIFFRACTION100
2.7839-2.89530.2661490.19062577X-RAY DIFFRACTION100
2.8953-3.02710.21961420.17662591X-RAY DIFFRACTION100
3.0271-3.18660.22711260.17192611X-RAY DIFFRACTION100
3.1866-3.38620.18861450.17952586X-RAY DIFFRACTION100
3.3862-3.64760.20721410.16812642X-RAY DIFFRACTION100
3.6476-4.01450.22211290.16592629X-RAY DIFFRACTION100
4.0145-4.59490.17511260.16142668X-RAY DIFFRACTION100
4.5949-5.78730.21631280.18392703X-RAY DIFFRACTION100
5.7873-46.02880.19911570.19362792X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -42.6421 Å / Origin y: -1.6742 Å / Origin z: -14.2909 Å
111213212223313233
T0.2343 Å20.008 Å20.018 Å2-0.2279 Å2-0.0153 Å2--0.2105 Å2
L0.4293 °2-0.015 °20.1683 °2-0.4094 °20.0754 °2--0.2783 °2
S0.0213 Å °0.0207 Å °0.0002 Å °-0.1202 Å °-0.0044 Å °-0.0589 Å °-0.0791 Å °-0.0094 Å °0 Å °
Refinement TLS groupSelection details: all

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