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- PDB-3i05: Tryptophanyl-tRNA synthetase from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 3i05
TitleTryptophanyl-tRNA synthetase from Trypanosoma brucei
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / apo tRNA-ligase / ATP-binding / Aminoacyl-tRNA synthetase / Nucleotide-binding / Protein biosynthesis / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytosol / 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-tRNA synthetase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArakaki, T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2011
Title: Crystal structures of three protozoan homologs of tryptophanyl-tRNA synthetase.
Authors: Merritt, E.A. / Arakaki, T.L. / Gillespie, R. / Napuli, A.J. / Kim, J.E. / Buckner, F.S. / Van Voorhis, W.C. / Verlinde, C.L. / Fan, E. / Zucker, F. / Hol, W.G.
History
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)90,2042
Polymers90,2042
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-24 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.294, 51.426, 89.970
Angle α, β, γ (deg.)95.290, 100.140, 106.050
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 400
2112B1 - 400

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Components

#1: Protein Tryptophanyl-tRNA synthetase


Mass: 45101.941 Da / Num. of mol.: 2 / Fragment: UNP residues 3-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb927.3.5580 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / References: UniProt: Q580R7, tryptophan-tRNA ligase

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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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.2 M Sodium Malonate, 20% PEG 3350, 1mM TCEP, pH 7.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorDetector: CCD / Date: Oct 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→30.76 Å / Num. obs: 20576 / % possible obs: 97.1 % / Redundancy: 3.07 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.077 / Χ2: 0.98 / Net I/σ(I): 9.2 / Scaling rejects: 478
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.8-2.93.080.3242.6635620531.1795.7
2.9-3.023.10.2623.1632920351.0695.4
3.02-3.153.080.213.763192041197.7
3.15-3.323.070.1744.4627720390.9796.7
3.32-3.533.070.1325.8630420430.9797
3.53-3.83.070.1086.9634620540.8897.1
3.8-4.183.050.06911.8634520660.9697.4
4.18-4.783.080.05414.8651921020.8798.1
4.78-6.023.070.05216640320720.998.7
6.02-30.763.010.03822.5640420711.0297.3

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
d*TREKdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2dr2

2dr2


Resolution: 2.8→30.76 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.871 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.219 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.748 / SU B: 42.09 / SU ML: 0.375 / SU R Cruickshank DPI: 0.371 / SU Rfree: 0.449 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1065 5.2 %RANDOM
Rwork0.241 ---
obs0.244 20555 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.81 Å2 / Biso mean: 5.391 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å21.18 Å20.91 Å2
2--1.21 Å21.93 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5199 0 0 0 5199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225350
X-RAY DIFFRACTIONr_bond_other_d0.0020.023630
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9547249
X-RAY DIFFRACTIONr_angle_other_deg0.92238808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0465655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3823.347242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49115870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5351532
X-RAY DIFFRACTIONr_chiral_restr0.0830.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215930
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021160
X-RAY DIFFRACTIONr_mcbond_it0.3671.53302
X-RAY DIFFRACTIONr_mcbond_other0.061.51317
X-RAY DIFFRACTIONr_mcangle_it0.68625321
X-RAY DIFFRACTIONr_scbond_it0.93332048
X-RAY DIFFRACTIONr_scangle_it1.5474.51928
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1919TIGHT POSITIONAL0.020.05
2380MEDIUM POSITIONAL0.030.5
1919TIGHT THERMAL0.635
2380MEDIUM THERMAL0.7510
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 72 -
Rwork0.365 1413 -
all-1485 -
obs--94.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.53313.00960.43816.96390.61111.2441-0.1217-0.316-1.1335-0.1724-0.3517-0.98551.36031.15840.47340.39910.33360.11030.62980.39470.724365.872-3.7771.204
28.4817-0.17642.03551.9328-1.04372.26690.083-0.7679-0.17360.0235-0.2770.05780.1870.02790.19410.37590.1860.03860.35780.05610.36947.4196.431-1.925
33.28493.73092.15855.61312.28973.8373-0.2241-0.2242-0.1551-0.39470.0363-0.1950.63580.34350.18780.48250.26210.08260.18690.07420.397844.7182.908-19.296
45.3983-4.7766-0.4096.682-3.48910.41180.35370.1401-0.5867-1.6237-0.78740.12481.23460.33910.43370.62220.3570.02360.53360.18680.44956.735.091-12.686
59.5161-1.473-1.77985.8202-6.68348.5576-0.8194-1.0256-1.17260.29810.25280.29851.0628-0.10450.56660.9049-0.01650.23280.77010.23060.689349.581-10.14512.706
66.9908-1.4486-1.33934.3578-2.51116.1824-0.2225-1.2306-0.38451.52390.47190.1824-0.8141-0.3388-0.24940.53360.065-0.08090.6885-0.09160.303747.8483.71912.163
710.1159-1.8464-1.85176.2095-2.56788.2594-0.07631.771-0.3674-0.70610.47210.83050.7368-2.1944-0.39570.3998-0.1897-0.14371.43860.46970.570911.14219.92-40.728
88.6312-0.70621.62031.1776-1.21714.92430.30631.14560.4225-0.18020.307-0.13660.0364-1.177-0.61340.33340.0493-0.00890.56550.30860.536920.86122.594-33.114
92.9829-0.529-1.68394.2888-1.07993.0204-0.01290.07950.1686-0.32780.17060.0820.3724-0.0672-0.15780.3280.0687-0.12190.16590.07420.358533.55215.215-25.614
102.23121.7953-2.79594.796-1.79499.7915-0.29431.142-0.3437-0.98520.1267-0.92032.241-0.90050.16750.7816-0.0632-0.09080.92030.29760.628325.91817.005-41.287
1114.85464.29254.08126.95761.080618.2123-0.40181.6382-0.122-0.89150.35290.4524-1.1882-1.0350.04890.78970.169-0.05711.56890.55740.710218.78529.916-58.178
126.29832.6024-0.43725.1212-3.19752.25250.78090.69281.0350.6216-0.00010.2906-1.45440.4652-0.78090.59150.18260.31280.13110.22990.837232.18133.697-34.595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 56
2X-RAY DIFFRACTION2A57 - 161
3X-RAY DIFFRACTION3A162 - 208
4X-RAY DIFFRACTION4A209 - 251
5X-RAY DIFFRACTION5A252 - 326
6X-RAY DIFFRACTION6A327 - 384
7X-RAY DIFFRACTION7B16 - 54
8X-RAY DIFFRACTION8B55 - 106
9X-RAY DIFFRACTION9B107 - 221
10X-RAY DIFFRACTION10B222 - 317
11X-RAY DIFFRACTION11B318 - 345
12X-RAY DIFFRACTION12B346 - 384

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