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- PDB-7a0p: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Comp... -

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Basic information

Entry
Database: PDB / ID: 7a0p
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11i
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-QTW / Leucine--tRNA ligase / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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
DepositionAug 10, 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 31, 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)99,0447
Polymers98,1851
Non-polymers8596
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint9 kcal/mol
Surface area34340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.004, 81.071, 225.110
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, 363 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-QTW / [(2~{R},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[3-[4-[(~{E})-phenylcarbonyliminomethyl]-1,2,3-triazol-1-yl]propyl]oxan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate


Mass: 582.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H38N6O8S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.28 Å3/Da / Density % sol: 45.98 % / Mosaicity: 0.17 °
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 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. ...Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with 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 11i in an equilvalent 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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980114 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980114 Å / Relative weight: 1
ReflectionResolution: 2.16→19.95 Å / Num. obs: 49494 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.057 / Rrim(I) all: 0.209 / Net I/σ(I): 9.1 / Num. measured all: 656160 / Scaling rejects: 1
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
2.16-2.2713.21.3919374771140.7110.3951.4472100
6.82-19.9511.60.0631942616700.9980.0190.06626.396.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q89

6q89


Resolution: 2.18→19.95 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 1995 4.17 %
Rwork0.196 45839 -
obs0.198 47834 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.82 Å2 / Biso mean: 41.1814 Å2 / Biso min: 14.93 Å2
Refinement stepCycle: final / Resolution: 2.18→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6310 0 54 357 6721
Biso mean--39.91 43.5 -
Num. residues----806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.18-2.230.31191380.239232563394
2.23-2.290.3421140.236232063320
2.29-2.360.31211260.23332563382
2.36-2.440.32641190.228732513370
2.44-2.530.271420.216832003342
2.53-2.630.2781480.21832563404
2.63-2.750.26681440.217432503394
2.75-2.890.27621450.209832593404
2.89-3.070.25861460.20832413387
3.07-3.310.27561450.20432483393
3.31-3.640.21331690.193332763445
3.64-4.160.22431440.175433013445
4.16-5.220.20811530.166833363489
5.22-19.950.21651620.188135033665
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)
10.75680.70330.56662.13530.20011.14330.05090.0474-0.14190.1207-0.0048-0.09190.12730.1123-0.06510.25660.0397-0.030.3098-0.02250.3114-2.6477-11.3052-38.5168
20.23920.0142-0.13220.94210.31640.5120.0238-0.0475-0.0052-0.0009-0.0140.0328-0.0710.0552-0.01350.220.0088-0.02350.316-0.01890.23833.052113.6871-24.4692
33.101-0.32931.30121.481-1.56253.57960.146-0.0756-0.2883-0.05740.03670.0877-0.07030.0425-0.15360.2977-0.00040.010.2704-0.03140.2931-9.841233.4091-10.8868
40.36550.0095-0.21140.56660.16760.68630.00340.02260.0417-0.03620.0343-0.0228-0.05070.0487-0.02880.2734-0.0225-0.02790.27670.01140.26042.503317.2351-28.0346
53.04691.3028-2.22982.059-1.79573.0027-0.2189-0.2509-0.32790.14740.09510.08910.2876-0.05730.01960.41070.0513-0.00540.3208-0.02950.2873-14.7356-8.3641-19.575
61.37960.27131.13341.74510.71332.5911-00.0360.034-0.04090.00990.1321-0.1075-0.0521-0.00530.1927-0.00820.0120.2143-0.02850.2334-21.926-17.6005-48.9696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 96 )A1 - 96
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 256 )A97 - 256
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 361 )A257 - 361
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 565 )A362 - 565
5X-RAY DIFFRACTION5chain 'A' and (resid 566 through 644 )A566 - 644
6X-RAY DIFFRACTION6chain 'A' and (resid 645 through 817 )A645 - 817

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