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

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Basic information

Entry
Database: PDB / ID: 6yku
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11f
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-OVB / Leucine--tRNA ligase / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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)99,0717
Polymers98,1851
Non-polymers8866
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint9 kcal/mol
Surface area36960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.109, 80.742, 224.012
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, 347 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 609.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34F3N5O8S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 341 / 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: 2.26 Å3/Da / Density % sol: 45.61 % / Mosaicity: 0.12 °
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 11f 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 1 / Wavelength: 0.978566 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978566 Å / Relative weight: 1
ReflectionResolution: 2.1→112.01 Å / Num. obs: 53182 / % possible obs: 99.6 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.031 / Rrim(I) all: 0.101 / Net I/σ(I): 14.3 / Num. measured all: 537780
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
2.1-2.21101.0387645676140.7430.3431.0952.199.3
6.63-112.0190.0341709118970.9990.0120.03644.499.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q89

6q89


Resolution: 2.14→65.498 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.77
RfactorNum. reflection% reflection
Rfree0.2312 2013 4.02 %
Rwork0.1785 --
obs0.1807 50028 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.97 Å2 / Biso mean: 48.9099 Å2 / Biso min: 21.75 Å2
Refinement stepCycle: final / Resolution: 2.14→65.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6514 0 55 341 6910
Biso mean--42.43 48.61 -
Num. residues----846
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.14-2.19350.291210.2233396100
2.1935-2.25280.26881230.2211335299
2.2528-2.31910.28161450.20793378100
2.3191-2.3940.2941490.209333799
2.394-2.47960.2461490.1975338499
2.4796-2.57880.26981450.19163395100
2.5788-2.69620.24811720.18793386100
2.6962-2.83840.24071480.18913366100
2.8384-3.01620.24791300.1833435100
3.0162-3.24910.23151490.183451100
3.2491-3.5760.23561360.1773437100
3.576-4.09340.21981470.16343500100
4.0934-5.15690.20761470.15563495100
5.1569-65.4980.2051520.183703100
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)
10.96110.59920.95761.55830.08831.69490.02470.097-0.21110.13350.0662-0.14170.25260.2768-0.07940.32410.0772-0.04920.3764-0.05490.3611-2.5811-11.4406-38.4558
21.17650.250.63690.57230.41721.14040.02340.1933-0.1620.09880.1022-0.14440.14260.1553-0.14290.31660.0612-0.04070.3922-0.02950.3359.5902-0.402-29.7035
30.1323-0.26880.56290.6204-0.5054.03450.0853-0.1072-0.03460.08330.05030.08860.1307-0.0481-0.1180.38070.0227-0.00410.4212-0.02850.36282.932414.0671-17.9923
40.5945-0.1199-0.47242.02531.29362.4120.08970.00080.09510.07210.04460.0027-0.40510.2383-0.09070.38180.0113-0.02640.30310.01060.3357-7.627633.0632-22.2614
53.4764-0.68980.26791.2347-1.42473.60250.12610.0211-0.33550.03480.05720.05170.01620.1803-0.16260.4257-0.0241-0.01280.3232-0.0290.3862-9.743232.2959-9.5665
61.5805-0.6463-0.57941.3964-0.40671.3270.18960.28720.1343-0.09070.01480.228-0.2403-0.2144-0.21350.41570.0093-0.05490.3033-0.03040.3703-16.393335.9587-24.8588
72.74251.940.57634.6914-0.36742.49320.1762-0.1107-0.06420.2831-0.032-0.17820.05280.2407-0.12760.29330.069-0.06450.4365-0.06060.366321.98634.9912-20.6694
81.42510.4261.03940.94810.39251.0371-0.0387-0.04-0.0522-0.06850.0807-0.0798-0.00320.1392-0.05580.27320.0261-0.02880.3572-0.00730.30348.12156.5614-35.7128
92.64780.84440.32121.74760.57210.16510.3382-0.5907-0.22350.7775-0.22960.2370.0393-0.04-0.11830.5067-0.0118-0.00380.4236-0.00410.3419-14.9568-9.1648-19.8209
101.5370.90550.66873.0221.57823.29380.2312-0.1232-0.00620.4025-0.17330.27880.3121-0.1845-0.04240.35030.02880.02010.29250.01520.3561-19.2437-19.6175-36.1401
113.95381.32371.86681.95941.09783.6419-0.04880.03110.2227-0.13930.01910.1791-0.1048-0.05450.04660.29070.0197-0.03910.2703-0.00730.3305-26.0659-16.4589-54.6278
121.64230.13920.32871.16970.2591.8555-0.07980.58450.0536-0.1309-0.02290.5518-0.2118-0.3477-0.11030.36660.0121-0.13730.6017-0.06190.5669-33.2839-11.935-61.7529
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 159 )A97 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 208 )A160 - 208
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 274 )A209 - 274
5X-RAY DIFFRACTION5chain 'A' and (resid 275 through 361 )A275 - 361
6X-RAY DIFFRACTION6chain 'A' and (resid 362 through 437 )A362 - 437
7X-RAY DIFFRACTION7chain 'A' and (resid 438 through 489 )A438 - 489
8X-RAY DIFFRACTION8chain 'A' and (resid 490 through 565 )A490 - 565
9X-RAY DIFFRACTION9chain 'A' and (resid 566 through 644 )A566 - 644
10X-RAY DIFFRACTION10chain 'A' and (resid 645 through 697 )A645 - 697
11X-RAY DIFFRACTION11chain 'A' and (resid 698 through 780 )A698 - 780
12X-RAY DIFFRACTION12chain 'A' and (resid 781 through 876 )A781 - 876

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