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- PDB-5thl: Crystal structure of the human tyrosyl-tRNA synthetase mutant G41R -

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Basic information

Entry
Database: PDB / ID: 5thl
TitleCrystal structure of the human tyrosyl-tRNA synthetase mutant G41R
ComponentsTyrosine--tRNA ligase, cytoplasmic
KeywordsLIGASE / Tyrosyl-tRNA synthetase / CMT / mutant
Function / homology
Function and homology information


interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process ...interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process / extracellular space / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / 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 ...Tyrosine-tRNA ligase / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / 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 / Nucleic acid-binding, OB-fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBlocquel, D. / Sajish, M. / Yang, X.L.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Alternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy.
Authors: Blocquel, D. / Li, S. / Wei, N. / Daub, H. / Sajish, M. / Erfurth, M.L. / Kooi, G. / Zhou, J. / Bai, G. / Schimmel, P. / Jordanova, A. / Yang, X.L.
History
DepositionSep 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 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, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)42,2341
Polymers42,2341
Non-polymers00
Water6,972387
1
A: Tyrosine--tRNA ligase, cytoplasmic

A: Tyrosine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)84,4672
Polymers84,4672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3010 Å2
ΔGint-25 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.846, 162.954, 35.492
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

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Components

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


Mass: 42233.699 Da / Num. of mol.: 1 / Mutation: G41R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YARS / Production host: Escherichia coli (E. coli) / References: UniProt: P54577, tyrosine-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: ammonium sulfate, acetone, sodium phosphate

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 57743 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.077 / Χ2: 2.018 / Net I/av σ(I): 39.789 / Net I/σ(I): 11.4 / Num. measured all: 392235
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.633.90.47193.5
1.63-1.664.30.44196.9
1.66-1.6950.398198.8
1.69-1.725.80.352199.9
1.72-1.767.20.311100
1.76-1.87.30.2651100
1.8-1.857.30.2281100
1.85-1.97.30.1891100
1.9-1.957.30.161100
1.95-2.027.30.1391100
2.02-2.097.40.1251100
2.09-2.177.30.1151100
2.17-2.277.30.1061100
2.27-2.397.30.1031100
2.39-2.547.40.0941100
2.54-2.747.30.0811100
2.74-3.017.30.0731100
3.01-3.457.30.0681100
3.45-4.347.20.0611100
4.34-506.80.052199.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N3L

1n3l


Resolution: 1.6→31.989 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 0 / Phase error: 19.18
RfactorNum. reflection% reflection
Rfree0.1956 2911 5.07 %
Rwork0.1853 --
obs0.1858 57365 99.47 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 37.304 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 71.87 Å2 / Biso mean: 24.9432 Å2 / Biso min: 10.33 Å2
Baniso -1Baniso -2Baniso -3
1-4.1124 Å2-0 Å2-0 Å2
2---4.0115 Å20 Å2
3----0.1008 Å2
Refinement stepCycle: final / Resolution: 1.6→31.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 0 387 3030
Biso mean---33.09 -
Num. residues----330

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