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- PDB-5ijx: Crystal Structure of a C-terminally truncated Coccidioides posada... -

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Basic information

Entry
Database: PDB / ID: 5ijx
TitleCrystal Structure of a C-terminally truncated Coccidioides posadasii 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


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding
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
Similarity search - Component
Biological speciesCoccidioides posadasii
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.63 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 Coccidioides posadasii mitochondrial tyrosyl-tRNA synthetase
Authors: Lamech, L.T. / Saoji, M. / Paukstelis, P.J. / Lambowitz, A.M.
History
DepositionMar 2, 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 1.3Mar 4, 2020Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rsym_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,3072
Polymers44,1261
Non-polymers1811
Water28816
1
A: Tyrosine--tRNA ligase, mitochondrial
hetero molecules

A: Tyrosine--tRNA ligase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6144
Polymers88,2512
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2620 Å2
ΔGint-26 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.173, 75.785, 52.316
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 44125.652 Da / Num. of mol.: 1 / Fragment: UNP residues 47-429
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides posadasii (strain C735) (fungus)
Strain: C735 / Gene: CPC735_063460 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: C5P455, 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.: 16 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10 mM HEPES-NaOH pH 7.0, 8% PEG 3350, 1% isopropanol, 1 mM L-tyrosine, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.63→30 Å / Num. obs: 12810 / % possible obs: 94.1 % / Redundancy: 6.6 % / Rsym value: 0.061 / Net I/σ(I): 40.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.63→27.679 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 27.63
RfactorNum. reflection% reflection
Rfree0.2356 622 4.86 %
Rwork0.2064 --
obs0.2079 12802 93.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.63→27.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 13 16 2820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022881
X-RAY DIFFRACTIONf_angle_d0.543910
X-RAY DIFFRACTIONf_dihedral_angle_d10.6131684
X-RAY DIFFRACTIONf_chiral_restr0.039420
X-RAY DIFFRACTIONf_plane_restr0.003506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6304-2.89480.32031140.26262459X-RAY DIFFRACTION76
2.8948-3.31310.29981680.23023209X-RAY DIFFRACTION99
3.3131-4.17190.24231750.19613222X-RAY DIFFRACTION100
4.1719-27.68090.20651650.19973290X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 32.2811 Å / Origin y: 4.4558 Å / Origin z: 16.8284 Å
111213212223313233
T0.554 Å2-0.0067 Å2-0.0143 Å2-0.4729 Å2-0.0697 Å2--0.6059 Å2
L2.9049 °20.0942 °20.7785 °2-1.6528 °20.3326 °2--2.0896 °2
S0.1388 Å °-0.0617 Å °0.0512 Å °-0.1345 Å °-0.257 Å °0.5794 Å °0.0212 Å °-0.2486 Å °0.1027 Å °
Refinement TLS groupSelection details: all

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