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- PDB-3kt8: Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase i... -

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Basic information

Entry
Database: PDB / ID: 3kt8
TitleCrystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with L-tryptophanamide
ComponentsTryptophanyl-tRNA synthetase, cytoplasmic
KeywordsLIGASE / tryptophanyl-tRNA synthetase / S. cerevisiae / sulfate ion / amino acid activation / catalytic mechanism / tryptophanamide / 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
L-TRYPTOPHANAMIDE / Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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)202,76618
Polymers200,9924
Non-polymers1,77414
Water37821
1
A: Tryptophanyl-tRNA synthetase, cytoplasmic
B: Tryptophanyl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,47910
Polymers100,4962
Non-polymers9838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-18 kcal/mol
Surface area34600 Å2
MethodPISA
2
C: Tryptophanyl-tRNA synthetase, cytoplasmic
D: Tryptophanyl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2878
Polymers100,4962
Non-polymers7916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-16 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)252.260, 252.260, 111.376
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-LTN / L-TRYPTOPHANAMIDE


Mass: 203.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13N3O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 5.089597 Å3/Da / Density % sol: 75.833054 % / Mosaicity: 0.757 °
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: 3→50 Å / Num. obs: 79287 / % possible obs: 97.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.117 / Χ2: 1.604 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.115.40.50776730.61295.1
3.11-3.235.40.36276790.82195.7
3.23-3.385.40.28877421.05595.9
3.38-3.565.50.23178341.40197.3
3.56-3.785.50.18979111.85697.9
3.78-4.075.60.15679822.24798.8
4.07-4.485.80.13480382.4599.4
4.48-5.1360.11280742.27999.7
5.13-6.466.20.09481401.75999.8
6.46-5060.05382141.27199.1

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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: 3→49.04 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0.65 / SU B: 15.77 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.585 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27307 3988 5 %RANDOM
Rwork0.24678 ---
obs0.24808 75143 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 193.48 Å2 / Biso mean: 80.62 Å2 / Biso min: 36.08 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å2-1.65 Å20 Å2
2---3.3 Å20 Å2
3---4.94 Å2
Refinement stepCycle: LAST / Resolution: 3→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13091 0 110 21 13222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02213523
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8571.96618255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7351620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22324.374647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.229152376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3511564
X-RAY DIFFRACTIONr_chiral_restr0.0590.21941
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210280
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1550.26361
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.29343
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0590.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2321.58332
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.436213156
X-RAY DIFFRACTIONr_scbond_it0.16535804
X-RAY DIFFRACTIONr_scangle_it0.2614.55099
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 271 -
Rwork0.357 5350 -
all-5621 -
obs--94.89 %

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