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- PDB-4j75: Crystal Structure of a parasite tRNA synthetase, product-bound -

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Basic information

Entry
Database: PDB / ID: 4j75
TitleCrystal Structure of a parasite tRNA synthetase, product-bound
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / aminoacyl-tRNA synthetase / aaRS / TrpRS / parasite / protein-substrate complex / Rossmann fold / translation / nucleotide binding
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / 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) / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle ...Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / 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
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKoh, C.Y. / Kim, J.E. / Verlinde, C.L.M.J. / Hol, W.G.J.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2013
Title: Crystal structures of Plasmodium falciparum cytosolic tryptophanyl-tRNA synthetase and its potential as a target for structure-guided drug design.
Authors: Koh, C.Y. / Kim, J.E. / Napoli, A.J. / Verlinde, C.L. / Fan, E. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G.
History
DepositionFeb 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3May 27, 2015Group: Structure summary
Revision 1.4Sep 20, 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
B: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6856
Polymers94,4332
Non-polymers1,2514
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-26 kcal/mol
Surface area30890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.033, 189.473, 51.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Tryptophanyl-tRNA synthetase / Tryptophan--tRNA ligase


Mass: 47216.734 Da / Num. of mol.: 2 / Fragment: UNP residues 229-632
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF13_0205 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IDW3, tryptophan-tRNA ligase
#2: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N7O8P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 15, 2010
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→38.64 Å / Num. obs: 45354 / % possible obs: 99.2 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 12.5
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 2.2 / Num. measured all: 32129 / Num. unique all: 4348 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.98 Å38.64 Å
Translation7.98 Å38.64 Å

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Processing

Software
NameVersionClassificationNB
Aimless0.1.27data scaling
PHASER2.5.2phasing
REFMACrefmac_5.7.0032refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4J76

4j76


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.471 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 2309 5.1 %RANDOM
Rwork0.1929 ---
obs0.1944 45312 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.41 Å2 / Biso mean: 43.9496 Å2 / Biso min: 13.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0 Å2
2---0.41 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6073 0 86 213 6372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196312
X-RAY DIFFRACTIONr_bond_other_d0.0030.025982
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9748516
X-RAY DIFFRACTIONr_angle_other_deg0.911313812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03424.885305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3911518
X-RAY DIFFRACTIONr_chiral_restr0.0640.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217044
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021512
X-RAY DIFFRACTIONr_mcbond_it0.7111.9072971
X-RAY DIFFRACTIONr_mcbond_other0.7091.9062966
X-RAY DIFFRACTIONr_mcangle_it1.2352.8553702
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 180 -
Rwork0.277 3093 -
all-3273 -
obs--97.96 %
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)
16.04860.5263-0.29859.838-2.21920.5132-0.15140.4030.2955-0.63790.371.01370.1288-0.1236-0.21850.20270.00930.02010.2172-0.00690.36214.76411.5236.288
21.4909-0.3731-0.75021.05770.28761.3875-0.02730.06430.11110.00830.04210.179-0.0865-0.1355-0.01470.0213-0.0049-0.00740.0390.02010.054322.2093.9671.615
33.3147-3.80771.29746.8737-1.47811.3365-0.10140.05770.63260.02730.0192-0.0142-0.260.04940.08220.2142-0.03090.00270.17640.01020.360618.28627.058.298
40.63021.1784-0.58637.5632.8934.0157-0.23840.2624-0.1494-1.14870.7868-0.7527-0.15380.4722-0.54840.3760.12080.12710.6994-0.32820.507158.27-21.202-24.163
52.532-0.4340.0981.8183-0.06670.90260.00250.1864-0.2883-0.1762-0.0035-0.13760.23560.02650.00110.0809-0.00830.01990.0437-0.0230.05344.485-14.936-11.943
62.04560.1620.18024.85981.51633.21010.01570.5289-0.7585-0.82540.1171-0.11260.4605-0.0493-0.13280.42620.0066-0.06230.3208-0.08270.492347.702-37.345-17.89
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A244 - 280
2X-RAY DIFFRACTION2A281 - 485
3X-RAY DIFFRACTION3A486 - 632
4X-RAY DIFFRACTION4B244 - 281
5X-RAY DIFFRACTION5B282 - 486
6X-RAY DIFFRACTION6B487 - 632

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