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

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Basic information

Entry
Database: PDB / ID: 6ykk
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 15
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 editing activity / ATP binding / cytoplasm
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-OVK / Leucine--tRNA ligase / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.236 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)98,9607
Polymers98,1851
Non-polymers7746
Water6,089338
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 area36200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.165, 80.973, 224.022
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, 344 molecules

#2: Chemical ChemComp-OVK / [(2~{R},3~{S},4~{R},5~{S})-3,4-bis(oxidanyl)-5-[2-(5-phenyl-1,2,3,4-tetrazol-2-yl)ethyl]oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate


Mass: 498.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N6O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / 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.: 338 / 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: 2.27 Å3/Da / Density % sol: 45.83 % / Mosaicity: 0.13 °
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 15 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: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.236→112.011 Å / Num. obs: 44350 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.078 / Rrim(I) all: 0.221 / Net I/σ(I): 8.5
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
2.24-2.368.41.4485372863590.6830.5181.5392.2100
7.07-112.017.20.0841135715850.9940.0320.0919.999.8

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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: 2.236→112.011 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.69
RfactorNum. reflection% reflection
Rfree0.2308 2028 4.58 %
Rwork0.1896 --
obs0.1915 44269 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 186.95 Å2 / Biso mean: 42.913 Å2 / Biso min: 17.9 Å2
Refinement stepCycle: final / Resolution: 2.236→112.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6392 0 48 339 6779
Biso mean--39.92 43.58 -
Num. residues----826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2364-2.29230.28521390.23722924
2.2923-2.35430.29911410.23492987
2.3543-2.42360.29261440.22242960
2.4236-2.50180.27671640.22472963
2.5018-2.59130.27121450.22012998
2.5913-2.6950.25011340.22112981
2.695-2.81770.30821290.22982976
2.8177-2.96630.25811630.20912989
2.9663-3.15210.24051440.19063009
3.1521-3.39550.22551460.18843021
3.3955-3.73720.21121340.17113039
3.7372-4.2780.19331420.15463048
4.278-5.38990.17161520.16333096
5.3899-112.0110.24191510.19213250
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)
11.26171.10980.97261.57210.62021.16490.07370.0588-0.1660.12450.0582-0.15370.28680.1834-0.13220.2750.0469-0.04010.2647-0.03370.304-2.6817-11.3309-38.316
20.3291-0.0512-0.00180.64140.50750.80170.0311-0.0112-0.039-0.00410.00610.07120.03390.0483-0.03020.2302-0.0001-0.03350.2945-0.00590.29723.5739.2363-26.0261
31.2994-0.2853-0.66030.4640.09871.41570.1176-0.06290.01120.02970.05810.108-0.2720.0223-0.17090.4183-0.0168-0.01880.2616-0.0180.3747-11.300835.6132-16.2425
41.76340.64271.02540.86710.33331.24650.0277-0.03090.00910.05930.0411-0.12550.10380.2386-0.0640.24780.0287-0.00530.2995-0.02070.27813.49355.9462-29.5826
52.16920.2483-1.03711.3355-0.74142.26180.0321-0.5564-0.20170.4103-0.07710.19380.14190.14620.04690.51470.0072-0.02430.4443-0.04240.288-14.1295-8.0336-20.2419
61.61330.55910.7551.79170.51272.11420.0656-0.05150.04040.0388-0.02010.22870.0915-0.0884-0.03650.19840.0101-0.00010.1895-0.03250.2629-23.3404-17.7274-47.1057
70.8007-0.13220.59990.6333-0.09751.7518-0.1260.3743-0.0707-0.17760.06230.34250.0435-0.1966-0.01180.3207-0.0727-0.15480.5059-0.01040.4769-27.3182-13.0746-59.393
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 235 )A97 - 235
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 437 )A236 - 437
4X-RAY DIFFRACTION4chain 'A' and (resid 438 through 564 )A438 - 564
5X-RAY DIFFRACTION5chain 'A' and (resid 565 through 644 )A565 - 644
6X-RAY DIFFRACTION6chain 'A' and (resid 645 through 780 )A645 - 780
7X-RAY DIFFRACTION7chain 'A' and (resid 781 through 849 )A781 - 849

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