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- PDB-3kt3: Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase i... -

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Basic information

Entry
Database: PDB / ID: 3kt3
TitleCrystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with TrpAMP
ComponentsTryptophanyl-tRNA synthetase, cytoplasmic
KeywordsLIGASE / tryptophanyl-tRNA synthetase / S. cerevisiae / sulfate ion / amino acid activation / catalytic mechanism / 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
TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
B: Tryptophanyl-tRNA synthetase, cytoplasmic
C: Tryptophanyl-tRNA synthetase, cytoplasmic
D: Tryptophanyl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,37521
Polymers200,9924
Non-polymers3,38317
Water3,207178
1
A: Tryptophanyl-tRNA synthetase, cytoplasmic
B: Tryptophanyl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,23511
Polymers100,4962
Non-polymers1,7399
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-20 kcal/mol
Surface area34300 Å2
MethodPISA
2
C: Tryptophanyl-tRNA synthetase, cytoplasmic
D: Tryptophanyl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,13910
Polymers100,4962
Non-polymers1,6438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-18 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)251.759, 251.759, 111.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 50248.094 Da / Num. of mol.: 4
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-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H24N7O8P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 5.056929 Å3/Da / Density % sol: 75.676941 % / Mosaicity: 0.608 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.1M HEPES, 2.2M (NH4)2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 118348 / % possible obs: 96.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.056 / Χ2: 0.94 / Net I/σ(I): 22.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.692.30.344102020.9683.4
2.69-2.82.50.252108410.87888.8
2.8-2.932.80.194114970.88493.7
2.93-3.083.40.146119130.94397.4
3.08-3.284.10.105121980.99299.5
3.28-3.534.90.086122591.079100
3.53-3.885.70.07122461.108100
3.88-4.456.20.058123381.073100
4.45-5.66.30.048123510.888100
5.6-506.20.032125030.60599.8

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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
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KT0

3kt0


Resolution: 2.6→48.94 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 17.308 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23672 5918 5 %RANDOM
Rwork0.21421 ---
obs0.21535 112240 96.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.02 Å2 / Biso mean: 53.4 Å2 / Biso min: 26.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-1.04 Å20 Å2
2---2.08 Å20 Å2
3---3.12 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13105 0 213 178 13496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02213649
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.97718449
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.12751622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77924.374647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.266152378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4771564
X-RAY DIFFRACTIONr_chiral_restr0.0730.21965
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210332
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.26465
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.29398
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2466
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3421.58312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.938213173
X-RAY DIFFRACTIONr_scbond_it3.88835963
X-RAY DIFFRACTIONr_scangle_it4.9194.55276
X-RAY DIFFRACTIONr_rigid_bond_restr4.151314275
X-RAY DIFFRACTIONr_sphericity_free0.6693178
X-RAY DIFFRACTIONr_sphericity_bonded1.522313318
LS refinement shellResolution: 2.602→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 372 -
Rwork0.328 7076 -
all-7448 -
obs--82.38 %

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