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- PDB-1r6t: crystal structure of human tryptophanyl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 1r6t
Titlecrystal structure of human tryptophanyl-tRNA synthetase
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / Class Ic tRNA synthetase / Rossmann fold catalytical domain / anticodon recognition domain / bound Trp-AMP
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 / S15/NS1, RNA-binding / Aminoacyl-tRNA synthetase, class Ic ...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 / S15/NS1, RNA-binding / 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 / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsYang, X.-L. / Otero, F.J. / Skene, R.J. / McRee, D.E. / Ribas de Pouplana, L. / Schimmel, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains
Authors: Yang, X.-L. / Otero, F.J. / Skene, R.J. / McRee, D.E. / Schimmel, P. / Ribas De Pouplana, L.
History
DepositionOct 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophanyl-tRNA synthetase
B: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4695
Polymers108,7512
Non-polymers7183
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-25 kcal/mol
Surface area33460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.146, 95.713, 98.506
Angle α, β, γ (deg.)90.00, 91.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tryptophanyl-tRNA synthetase / Tryptophan--tRNA ligase / TrpRS / IFP53 / hWRS


Mass: 54375.602 Da / Num. of mol.: 2 / Mutation: S213G, Y214D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WARS / Plasmid: pET20b+ / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P23381, tryptophan-tRNA ligase
#2: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.32
Details: PEG 8K, Mes, pH 6.32, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 %PEG80001reservoir
20.1 Msodium-MES1reservoirpH6.32
310 mMHEPES1droppH7.5
420 mM1dropKCl
50.02 %1dropNaN3
62 mM2-mercaptoethanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97941 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2002
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 162039 / Num. obs: 153937 / % possible obs: 95 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 13.87
Reflection shellResolution: 2.1→2.17 Å / % possible all: 87.3
Reflection
*PLUS
Num. obs: 82479 / % possible obs: 96.5 %
Reflection shell
*PLUS
% possible obs: 87.3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1

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Processing

Software
NameClassification
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2386 6915 Random
Rwork0.208 --
all0.2082 162215 -
obs0.2082 139484 -
Solvent computationBsol: 45.2541 Å2 / ksol: 0.341653 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.024 Å20 Å2-8.367 Å2
2---3.98 Å20 Å2
3---0.956 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6435 0 49 294 6778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna.param
X-RAY DIFFRACTION3WPA.param
X-RAY DIFFRACTION4goln.param
X-RAY DIFFRACTION5water_rep.param
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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