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- PDB-2quh: Crystal structures of human tryptophanyl-tRNA synthetase in compl... -

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Basic information

Entry
Database: PDB / ID: 2quh
TitleCrystal structures of human tryptophanyl-tRNA synthetase in complex with Trp
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / Aminoacyl-tRNA synthetase / Rossmann fold / induced-fit mechnism / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / angiogenesis / translation ...tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / angiogenesis / translation / negative regulation of cell population proliferation / protein domain specific binding / 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 / Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShen, N. / Ding, J.P.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states
Authors: Shen, N. / Zhou, M. / Yang, B. / Yu, Y. / Dong, X. / Ding, J.
History
DepositionAug 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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)108,5294
Polymers108,1202
Non-polymers4082
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24.2 kcal/mol
Surface area30120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.9, 79.9, 382.3
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 54060.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WARS, IFI53, WRS / Plasmid: pET24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23381, tryptophan-tRNA ligase
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.0M Na Citrate, 100mM HEPES, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 43430 / % possible obs: 86.7 % / Redundancy: 10.1 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 12.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 1 / % possible all: 46.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O5T

1o5t


Resolution: 2.4→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3252313.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2168 5 %RANDOM
Rwork0.207 ---
obs0.207 43267 86.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.0359 Å2 / ksol: 0.361236 e/Å3
Displacement parametersBiso mean: 46.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.55 Å20 Å20 Å2
2--6.92 Å20 Å2
3----13.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 30 278 6394
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 190 4.8 %
Rwork0.35 3787 -
obs--48.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3lig.paramlig.top
X-RAY DIFFRACTION4ion.paramion.top

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