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- PDB-5fod: Crystal structure of the P.falciparum cytosolic leucyl-tRNA synth... -

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Basic information

Entry
Database: PDB / ID: 5fod
TitleCrystal structure of the P.falciparum cytosolic leucyl-tRNA synthetase editing domain (space group P1) containing deletions of insertions 1 and 3
ComponentsLEUCYL-TRNA SYNTHETASE
KeywordsLIGASE / P.FALCIPARUM / LEUCINE-TRNA LIGASE (LEURS) ACTIVITY / ATP + L-LEUCINE + TRNA(LEUCINE) GIVES AMP + DIPHOSPHATE + L-LEUCYL-TRNA(LEUCINE) / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS / NOVEL BORON INHIBITORS OF LEURS
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / cytoplasm
Similarity search - Function
Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
leucine--tRNA ligase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPalencia, A. / Sonoiki, E. / Guo, D. / Ahyong, V. / Dong, C. / Li, X. / Hernandez, V.S. / Gut, J. / Legac, J. / Cooper, R. ...Palencia, A. / Sonoiki, E. / Guo, D. / Ahyong, V. / Dong, C. / Li, X. / Hernandez, V.S. / Gut, J. / Legac, J. / Cooper, R. / Alley, M.R.K. / Freund, Y.R. / DeRisi, J. / Cusack, S. / Rosenthal, P.J.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2016
Title: Anti-Malarial Benzoxaboroles Target P. Falciparum Leucyl-tRNA Synthetase.
Authors: Sonoiki, E. / Palencia, A. / Guo, D. / Ahyong, V. / Dong, C. / Li, X. / Hernandez, V.S. / Zhang, Y.K. / Choi, W. / Gut, J. / Legac, J. / Cooper, R. / Alley, M.R. / Freund, Y.R. / Derisi, J. ...Authors: Sonoiki, E. / Palencia, A. / Guo, D. / Ahyong, V. / Dong, C. / Li, X. / Hernandez, V.S. / Zhang, Y.K. / Choi, W. / Gut, J. / Legac, J. / Cooper, R. / Alley, M.R. / Freund, Y.R. / Derisi, J. / Cusack, S. / Rosenthal, P.J.
History
DepositionNov 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: LEUCYL-TRNA SYNTHETASE
B: LEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7293
Polymers79,6672
Non-polymers621
Water3,153175
1
A: LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)39,8331
Polymers39,8331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8952
Polymers39,8331
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.600, 53.100, 62.700
Angle α, β, γ (deg.)88.40, 73.70, 89.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein LEUCYL-TRNA SYNTHETASE


Mass: 39833.352 Da / Num. of mol.: 2
Fragment: EDITING DOMAIN, UNP RESIDUES 274-329,361-474,521-687
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): DE3 RIL / References: UniProt: C6KT64, leucine-tRNA ligase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES (PH 7.5), 20% (W/V) PEG 10000, AND 8% ETHYLENEGLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 62051 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 0.8 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PLASMODIUM KNOWLESI LEURS EDITING DOMAIN

Resolution: 1.7→60.16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.95 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. PRESENCE OF NCS
RfactorNum. reflection% reflectionSelection details
Rfree0.25506 3020 4.9 %RANDOM
Rwork0.20262 ---
obs0.20517 59030 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20.43 Å2-0.83 Å2
2---0.11 Å2-0.43 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.7→60.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5093 0 4 175 5272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.025232
X-RAY DIFFRACTIONr_bond_other_d0.0020.024977
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9687050
X-RAY DIFFRACTIONr_angle_other_deg0.985311534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2525627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20725.873252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.519151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.518158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025851
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021181
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5733.1192486
X-RAY DIFFRACTIONr_mcbond_other2.5663.1182485
X-RAY DIFFRACTIONr_mcangle_it3.7034.6563101
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4053.5762746
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 238 -
Rwork0.381 4117 -
obs--88.75 %

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