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- PDB-5thh: Crystal structure of a human tyrosyl-tRNA synthetase mutant -

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Basic information

Entry
Database: PDB / ID: 5thh
TitleCrystal structure of a human tyrosyl-tRNA synthetase mutant
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 / RNA binding / extracellular space / 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 ...: / 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 / Tyrosine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.959 Å
AuthorsBlocquel, D. / 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 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5742
Polymers38,3921
Non-polymers1811
Water5,188288
1
A: Tyrosine--tRNA ligase, cytoplasmic
hetero molecules

A: Tyrosine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1474
Polymers76,7852
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area2730 Å2
ΔGint-23 kcal/mol
Surface area29420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.238, 75.705, 163.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

21A-675-

HOH

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Components

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


Mass: 38392.469 Da / Num. of mol.: 1 / Mutation: E196K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YARS
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P54577, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H11NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
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: BL7-1 / Wavelength: 1.07808 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07808 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 33334 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.05 / Rrim(I) all: 0.132 / Χ2: 2.596 / Net I/av σ(I): 28.657 / Net I/σ(I): 7.9 / Num. measured all: 231392
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-1.976.30.80916040.6620.3440.8812.11998.8
1.97-2.0170.69816060.8550.2810.7531.70799.9
2.01-2.0570.48216640.9010.1960.5210.90599.9
2.05-2.0970.51416550.9350.2070.5551.415100
2.09-2.1470.42316110.9510.1720.4571.367100
2.14-2.1870.47416530.9420.1890.512.273100
2.18-2.2470.36816450.9540.1510.3992.06100
2.24-2.37.10.25616350.9730.1030.2761.3299.8
2.3-2.377.10.36816720.9440.150.3983.05499.6
2.37-2.447.10.23116310.9320.0920.2491.88999.8
2.44-2.537.10.22616670.9860.0890.2441.97599.8
2.53-2.637.10.2616160.9860.1030.283.05199.6
2.63-2.757.10.19816680.3170.0840.2162.39899.7
2.75-2.97.10.14816830.9910.060.162.791100
2.9-3.0870.14716670.9620.0590.1593.88999.9
3.08-3.3270.10916850.9930.0440.1184.21499.9
3.32-3.6570.08816970.9950.0350.0954.04599.9
3.65-4.186.90.07717150.9950.0310.0834.22599.9
4.18-5.266.50.0717160.9950.0290.0764.20799.5
5.26-506.50.06318440.9940.0270.0692.87898.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N3L

1n3l


Resolution: 1.959→37.852 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 1998 6.21 %
Rwork0.1778 30201 -
obs0.1804 32199 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.48 Å2 / Biso mean: 40.461 Å2 / Biso min: 16.21 Å2
Refinement stepCycle: final / Resolution: 1.959→37.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 13 288 2931
Biso mean--25.49 45.05 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182716
X-RAY DIFFRACTIONf_angle_d1.6163670
X-RAY DIFFRACTIONf_chiral_restr0.086411
X-RAY DIFFRACTIONf_plane_restr0.009462
X-RAY DIFFRACTIONf_dihedral_angle_d14.8081034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9593-2.00830.29811270.24141925205292
2.0083-2.06260.27141440.206121682312100
2.0626-2.12330.26391410.197321222263100
2.1233-2.19180.24221420.1921512293100
2.1918-2.27010.22841390.181721092248100
2.2701-2.3610.21511440.183721642308100
2.361-2.46840.26351410.183821382279100
2.4684-2.59860.2331430.180321512294100
2.5986-2.76130.22631420.190621462288100
2.7613-2.97440.23041450.194921872332100
2.9744-3.27360.24711440.187521732317100
3.2736-3.7470.21691440.162621932337100
3.747-4.71940.17991470.141822262373100
4.7194-37.85950.19041550.18522348250399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.07740.22430.44482.2122-0.15022.39320.08230.0183-0.14760.10530.0007-0.07930.20580.1114-0.0690.19420.0185-0.02010.1982-0.04050.2177-2.348126.7441-22.7517
21.66640.41440.76182.12481.20873.3810.0903-0.1512-0.04570.0941-0.07950.10220.0705-0.22920.00250.1858-0.0078-0.00580.1870.00130.1683-7.450232.9257-13.9821
32.37890.97782.13452.87662.17515.73030.1352-0.1593-0.26760.4284-0.1129-0.13880.4818-0.174-0.05430.27690.0174-0.02170.2228-0.02590.2825-11.10748.1597-32.1995
42.67783.81530.09375.53350.13380.4552-0.20140.3854-1.6932-0.18250.6186-1.36360.1836-0.3651-0.59780.1775-0.084-0.01240.32130.00340.3011-7.246228.8035-14.5079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 108 )A4 - 108
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 237 )A109 - 237
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 342 )A238 - 342
4X-RAY DIFFRACTION4chain 'A' and (resid 401 through 401 )B12

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