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- PDB-5uji: Crystal structure of human T2-Tryptophanyl-tRNA synthetase with H... -

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Basic information

Entry
Database: PDB / ID: 5uji
TitleCrystal structure of human T2-Tryptophanyl-tRNA synthetase with H130R mutation
ComponentsTryptophan--tRNA ligase, cytoplasmic
KeywordsLIGASE / Rossmann-fold catalytic domain / anti-codon binding domain / H130R mutation
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / positive regulation of protein-containing complex assembly / negative regulation of protein kinase activity / angiogenesis / translation ...tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / positive regulation of protein-containing complex assembly / negative regulation of protein kinase activity / angiogenesis / translation / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of gene expression / protein kinase binding / protein homodimerization activity / protein-containing complex / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) ...WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Tryptophan-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 / S15/NS1, RNA-binding / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsXu, X. / Yang, X.-L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31400630 China
Zhejiang Provincial Natural Science Foundation of ChinaLY14C050002 China
CitationJournal: RNA Biol / Year: 2018
Title: An alternative conformation of human TrpRS suggests a role of zinc in activating non-enzymatic function.
Authors: Xu, X. / Zhou, H. / Zhou, Q. / Hong, F. / Vo, M.N. / Niu, W. / Wang, Z. / Xiong, X. / Nakamura, K. / Wakasugi, K. / Schimmel, P. / Yang, X.L.
History
DepositionJan 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan--tRNA ligase, cytoplasmic
B: Tryptophan--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)89,2902
Polymers89,2902
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-21 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.888, 139.057, 146.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tryptophan--tRNA ligase, cytoplasmic / Interferon-induced protein 53 / IFP53 / Tryptophanyl-tRNA synthetase / hWRS


Mass: 44644.906 Da / Num. of mol.: 2 / Fragment: UNP residues 56-430 / Mutation: H130R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WARS, IFI53, WRS / Plasmid: pET20b / Details (production host): C-terminal His tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23381, tryptophan-tRNA ligase

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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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20 % PEG4000, 0.1 M Na Citrate pH5.0, 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.79→146 Å / Num. obs: 21588 / % possible obs: 98.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.093 / Rsym value: 0.078 / Net I/σ(I): 6.5
Reflection shellResolution: 2.79→2.85 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.471 / Num. unique all: 5436 / Num. unique obs: 1066 / Rsym value: 0.371 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
HKL-2000data processing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QUI

2qui


Resolution: 2.79→32.726 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / SU B: 19.126 / SU ML: 0.356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1085 5 %RANDOM
Rwork0.2187 ---
obs0.221 20481 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.27 Å2 / Biso mean: 72.222 Å2 / Biso min: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å2-0 Å2-0 Å2
2--7 Å20 Å2
3----5.11 Å2
Refinement stepCycle: final / Resolution: 2.79→32.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5752 0 0 0 5752
Num. residues----710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195884
X-RAY DIFFRACTIONr_bond_other_d0.0010.025614
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9547930
X-RAY DIFFRACTIONr_angle_other_deg0.906312924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65423.776286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.522151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9781537
X-RAY DIFFRACTIONr_chiral_restr0.0660.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021408
LS refinement shellResolution: 2.794→2.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 70 -
Rwork0.299 1398 -
all-1468 -
obs--93.32 %

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