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- PDB-3kt0: Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 3kt0
TitleCrystal structure of S. cerevisiae tryptophanyl-tRNA synthetase
ComponentsTryptophanyl-tRNA synthetase, cytoplasmic
KeywordsLIGASE / tryptophanyl-tRNA synthetase / Rossmann fold / S. cerevisiae / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / sequence-specific mRNA binding / ATP binding / cytoplasm
Similarity search - Function
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 / Rossmann fold ...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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EMN / Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhou, M. / Dong, X. / Zhong, C. / Shen, N. / Ding, J.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design
Authors: Zhou, M. / Dong, X. / Shen, N. / Zhong, C. / Ding, J.
History
DepositionNov 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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

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Assembly

Deposited unit
A: Tryptophanyl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4532
Polymers50,2481
Non-polymers2051
Water2,522140
1
A: Tryptophanyl-tRNA synthetase, cytoplasmic
hetero molecules

A: Tryptophanyl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9074
Polymers100,4962
Non-polymers4112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2960 Å2
ΔGint-15 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.912, 55.912, 313.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tryptophanyl-tRNA synthetase, cytoplasmic / Tryptophan--tRNA ligase / TrpRS


Mass: 50248.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: trpS / Plasmid: pET3E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12109, tryptophan-tRNA ligase
#2: Chemical ChemComp-EMN / (2S)-1-{[(2S)-3-(2-methoxyethoxy)-2-methylpropyl]oxy}propan-2-amine


Mass: 205.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H23NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND EMN IS A PART OF JEFFAMINE M-600 REAGENT.

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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: 2.44 Å3/Da / Density % sol: 49.59 % / Mosaicity: 1.57 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES buffer, 0.05M CsCl, 30% v/v Jeffamine M-600 reagent, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 29469 / % possible obs: 96.6 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.102 / Χ2: 1.142 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.189.50.58629110.8498.5
2.18-2.269.60.48929461.198.7
2.26-2.379.60.36429090.90798.7
2.37-2.499.50.2829570.93298.8
2.49-2.659.40.21329721.00798.9
2.65-2.859.30.15429451.09298.4
2.85-3.149.20.11830041.23898.6
3.14-3.598.90.08429961.48197.7
3.59-4.528.40.06428471.62291.7
4.52-507.80.04929821.32287.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O5T

1o5t


Resolution: 2.1→33.45 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 9.665 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1471 5 %RANDOM
Rwork0.207 ---
obs0.208 29427 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.68 Å2 / Biso mean: 37.426 Å2 / Biso min: 0.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å20 Å2
2--1.88 Å20 Å2
3----3.76 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 14 140 3179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223117
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.9654200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2835371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77724.133150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25815549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4371515
X-RAY DIFFRACTIONr_chiral_restr0.0760.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022366
X-RAY DIFFRACTIONr_nbd_refined0.1930.21466
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.213
X-RAY DIFFRACTIONr_mcbond_it1.4561.51918
X-RAY DIFFRACTIONr_mcangle_it1.9523017
X-RAY DIFFRACTIONr_scbond_it2.48631341
X-RAY DIFFRACTIONr_scangle_it3.9484.51183
X-RAY DIFFRACTIONr_rigid_bond_restr1.91333259
X-RAY DIFFRACTIONr_sphericity_free10.1123140
X-RAY DIFFRACTIONr_sphericity_bonded1.15733040
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 121 -
Rwork0.237 2058 -
all-2179 -
obs--98.2 %

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