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- PDB-6ykl: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Comp... -

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Basic information

Entry
Database: PDB / ID: 6ykl
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11k
ComponentsLeucine--tRNA ligase
KeywordsLIGASE / protein-inhibitor complex / Rossmann fold / tRNA synthetase
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / cytoplasm / cytosol
Similarity search - Function
Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / 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
Chem-OVH / Leucine--tRNA ligase / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsPang, L. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G077814N Belgium
Research Foundation - Flanders (FWO)G0A4616A Belgium
Research Foundation - Flanders (FWO)1109117N Belgium
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Synthesis and structure-activity studies of novel anhydrohexitol-based Leucyl-tRNA synthetase inhibitors.
Authors: De Ruysscher, D. / Pang, L. / Lenders, S.M.G. / Cappoen, D. / Cos, P. / Rozenski, J. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionApr 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9256
Polymers98,1851
Non-polymers7395
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint6 kcal/mol
Surface area36970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.402, 81.298, 225.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 98185.344 Da / Num. of mol.: 1 / Fragment: Leucyl-tRNA Synthetase / Mutation: D454N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: leuS, VT05_02036, WHOO_00006, WHOO_00455 / Plasmid: pETRUK / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS
References: UniProt: A0A5K1KQ39, UniProt: Q5FAJ3*PLUS, leucine-tRNA ligase

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Non-polymers , 5 types, 246 molecules

#2: Chemical ChemComp-OVH / [(2~{R},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[3-(4-phenyl-1,2,3-triazol-1-yl)propyl]oxan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate


Mass: 525.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H35N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with of 0.1 M Bis-tris propane pH 8.5, 0.1 M MgCl2, 20% w/v PEG 3350 and a crystal seed stock in ...Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with of 0.1 M Bis-tris propane pH 8.5, 0.1 M MgCl2, 20% w/v PEG 3350 and a crystal seed stock in a 0.75:1.0:0.25 (v/v) ratio. The seed stock was prepared in the same crystallization buffer. Suitable crystals were soaked with 2 mM synthesized compound 11k in an equivalent precipitant solution supplemented with 22% v/v Ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.27→76.47 Å / Num. obs: 42988 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.057 / Rrim(I) all: 0.149 / Net I/σ(I): 10.1 / Num. measured all: 287773 / Scaling rejects: 375
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.27-2.3971.0194311961750.680.4121.1012.4100
7.18-76.476.50.057987015300.9960.0230.06223.999.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q89

6q89


Resolution: 2.27→76.469 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.04
RfactorNum. reflection% reflection
Rfree0.2381 2075 4.84 %
Rwork0.1877 --
obs0.1902 42893 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.44 Å2 / Biso mean: 51.0876 Å2 / Biso min: 21.71 Å2
Refinement stepCycle: final / Resolution: 2.27→76.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6458 0 46 241 6745
Biso mean--51.36 49 -
Num. residues----841
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.27-2.32280.30851360.24262698100
2.3228-2.38090.29661640.24112631100
2.3809-2.44530.28361280.2322694100
2.4453-2.51720.281120.23222692100
2.5172-2.59850.31611280.2432715100
2.5985-2.69140.33361280.2462670100
2.6914-2.79910.3161330.2412733100
2.7991-2.92650.29981460.2288266599
2.9265-3.08080.24441370.2033269599
3.0808-3.27390.25811440.1942269899
3.2739-3.52660.22031550.18092713100
3.5266-3.88150.22691310.16472726100
3.8815-4.44310.18471460.14852761100
4.4431-5.59760.22051430.16092795100
5.5976-76.4690.20421440.1773293299
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)
10.31930.39390.11050.69820.28060.82580.0503-0.0058-0.08280.0789-0.0139-0.03980.08460.0884-0.04240.30660.0399-0.06520.3754-0.00560.35440.91774.1164-29.8073
23.0145-0.05540.40520.944-0.34232.88780.07690.0797-0.0769-0.01580.07580.1756-0.2909-0.0528-0.11210.40050.0110.00590.24920.01070.3283-14.614134.2722-13.5758
30.58410.0493-0.04040.58780.09780.87520.0329-0.05790.00120.02690.0478-0.0249-0.06480.1155-0.08440.29830.0151-0.02190.3457-0.00740.2878.438912.8252-29.5356
41.94730.6745-0.78521.5909-0.41131.47770.1469-0.2698-0.28660.4486-0.10140.11840.14730.08630.04360.47730.0312-0.04260.2966-0.00460.3677-14.6398-9.6838-20.4571
51.51220.39921.28031.83720.35232.15710.0502-0.09510.04450.0305-0.00630.2310.0188-0.1517-0.03180.26040.0076-0.01660.2549-0.02790.3171-23.4258-17.9531-47.3489
61.38210.08811.03840.9418-0.30041.9153-0.1070.2650.11910.01940.00840.3538-0.2495-0.21820.03780.42810.0594-0.11020.4755-0.08110.5078-32.9827-12.628-61.7948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 256 )A1 - 256
2X-RAY DIFFRACTION2chain 'A' and (resid 257 through 396 )A257 - 396
3X-RAY DIFFRACTION3chain 'A' and (resid 397 through 564 )A397 - 564
4X-RAY DIFFRACTION4chain 'A' and (resid 565 through 644 )A565 - 644
5X-RAY DIFFRACTION5chain 'A' and (resid 645 through 780 )A645 - 780
6X-RAY DIFFRACTION6chain 'A' and (resid 781 through 876 )A781 - 876

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