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

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Basic information

Entry
Database: PDB / ID: 6ykw
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11h
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-OVZ / Leucine--tRNA ligase / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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)98,9686
Polymers98,1851
Non-polymers7835
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint5 kcal/mol
Surface area37190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.429, 81.338, 225.620
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, 99 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-OVZ / [(2~{R},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[3-[4-[[(phenylmethyl)amino]methyl]-1,2,3-triazol-1-yl]propyl]oxan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate


Mass: 568.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N6O7S / Feature type: SUBJECT OF INVESTIGATION
#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.: 94 / 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: 2.31 Å3/Da / Density % sol: 46.75 % / Mosaicity: 0.22 °
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 11h 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: 0.980118 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980118 Å / Relative weight: 1
ReflectionResolution: 2.456→65.98 Å / Num. obs: 34241 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.035 / Rrim(I) all: 0.105 / Net I/σ(I): 13.4
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
2.46-2.599.41.1924606849010.7010.4071.2611.9100
7.77-65.988.20.0411023612430.9980.0150.04436.399.9

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Processing

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

6q89


Resolution: 2.46→65.977 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.05
RfactorNum. reflection% reflection
Rfree0.2412 1702 4.98 %
Rwork0.1988 --
obs0.201 34168 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.04 Å2 / Biso mean: 65.8891 Å2 / Biso min: 32.88 Å2
Refinement stepCycle: final / Resolution: 2.46→65.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6439 0 88 94 6621
Biso mean--60.55 55.27 -
Num. residues----839
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.46-2.52860.32081300.26442646
2.5286-2.61020.31311630.2512665
2.6102-2.70350.31151310.25282636
2.7035-2.81170.29731310.25122684
2.8117-2.93970.32751290.24952681
2.9397-3.09470.30331360.23642694
3.0947-3.28860.26981480.22022694
3.2886-3.54250.24691320.20842703
3.5425-3.89890.24921320.18752685
3.8989-4.4630.21081500.16982725
4.463-5.62250.1951650.17452741
5.6225-65.9770.2281550.18622912
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)
12.7631.72671.83241.6771.48441.84060.17140.1606-0.46550.25810.1604-0.36180.41020.3184-0.33870.45560.1043-0.13730.5185-0.06130.54891.5608-9.6876-36.465
20.7755-0.2609-0.34020.60850.56591.57110.07580.00360.13590.0143-0.06890.1192-0.21120.2064-0.00840.4123-0.0319-0.06530.4709-0.02410.52680.137622.1138-20.8551
36.83030.76952.48570.2987-0.10537.36560.1341-0.1972-0.48440.07140.0298-0.065-0.31170.1742-0.10520.5560.0081-0.00120.34380.01590.4895-10.236733.5633-10.9415
40.4631-0.04420.23920.61440.1770.71870.0370.0091-0.00020.15630.02990.07850.07840.0551-0.06970.3930.0233-0.03280.4330.00080.4047-8.92830.7222-33.5346
53.2974-0.74042.15631.211-0.83582.59070.1670.6185-0.19710.0205-0.13770.5602-0.0044-0.1068-0.0320.50850.0281-0.18240.6939-0.10850.7539-32.8623-12.6477-61.5539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 145 )A1 - 145
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 256 )A146 - 256
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 361 )A257 - 361
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 778 )A362 - 778
5X-RAY DIFFRACTION5chain 'A' and (resid 779 through 876 )A779 - 876

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