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

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Basic information

Entry
Database: PDB / ID: 6yks
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11d
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 / cytosol / 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-OVT / Leucine--tRNA ligase / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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)99,0157
Polymers98,1851
Non-polymers8306
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint9 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.023, 80.909, 224.177
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, 406 molecules

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


Mass: 553.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H39N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / 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 / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 45.67 % / 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 11d 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: 1.95→112.09 Å / Num. obs: 66445 / % possible obs: 99.9 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.028 / Rrim(I) all: 0.079 / Net I/σ(I): 14.6 / Num. measured all: 533986
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
1.95-2.057.60.8597210495330.7510.3280.9211.999.8
6.16-112.097.40.02817344234310.0110.0343.699.9

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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: 1.97→65.603 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.52
RfactorNum. reflection% reflection
Rfree0.2166 2082 3.25 %
Rwork0.1753 --
obs0.1766 64104 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.4 Å2 / Biso mean: 42.8199 Å2 / Biso min: 19.97 Å2
Refinement stepCycle: final / Resolution: 1.97→65.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6321 0 52 400 6773
Biso mean--45.58 47.06 -
Num. residues----813
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.97-2.01580.32061260.23674053
2.0158-2.06620.27481530.21464032
2.0662-2.12210.2681250.20274099
2.1221-2.18460.2411350.19064063
2.1846-2.25510.21821350.18464115
2.2551-2.33570.23931570.1824085
2.3357-2.42920.21211410.17234088
2.4292-2.53980.20921300.17554086
2.5398-2.67370.2291360.17774110
2.6737-2.84120.28011250.19314153
2.8412-3.06050.261290.18914166
3.0605-3.36850.22181350.18134152
3.3685-3.85590.1921620.16314167
3.8559-4.85780.17881380.14864228
4.8578-65.6030.20831550.17744425
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)
11.31521.17110.97961.19160.6580.88740.15370.1527-0.28590.20780.0967-0.20030.28020.1966-0.26060.29250.0712-0.06410.3068-0.06680.3271.6869-9.0869-36.4231
20.246-0.20160.1920.59050.27242.4650.0372-0.16360.04530.02560.0970.11040.1433-0.0914-0.07250.2612-0.0015-0.02620.3556-0.00110.30674.8414.9768-18.1165
30.91730.3945-0.22783.33872.24973.34280.0709-0.09140.1363-0.031-0.11130.2102-0.42920.16630.07160.2450.0051-0.04590.25630.0120.2814-5.8131.9592-23.6307
43.0058-0.64960.65511.4825-0.76713.18660.17980.028-0.1124-0.08690.01020.1465-0.07530.0048-0.18160.4006-0.03150.00180.2522-0.0250.3304-14.354934.2424-13.454
50.33020.08120.14360.52670.0690.7078-0.010.05120.00770.06780.0829-0.0727-0.06670.1863-0.08430.21-0.0026-0.01350.2865-0.01950.24268.484713.2555-29.2476
62.35010.07680.50141.240.481.20760.2928-0.6131-0.33480.8252-0.20360.16880.2039-0.103-0.05070.5734-0.0448-0.00930.3862-0.01080.3227-14.483-8.5142-20.3782
72.46730.9341.23662.8561.7463.98840.3055-0.2478-0.09940.5831-0.18840.21910.4366-0.2736-0.1410.3275-0.00880.01790.21970.01510.276-19.418-19.688-36.6045
83.00091.40911.80612.1541.37973.1434-0.09540.19850.1584-0.17060.09330.2099-0.07520.0602-0.00170.24920.0007-0.05590.2276-0.01530.289-23.3917-16.2546-55.0872
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 208 )A146 - 208
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 256 )A209 - 256
4X-RAY DIFFRACTION4chain 'A' and (resid 257 through 396 )A257 - 396
5X-RAY DIFFRACTION5chain 'A' and (resid 397 through 564 )A397 - 564
6X-RAY DIFFRACTION6chain 'A' and (resid 565 through 644 )A565 - 644
7X-RAY DIFFRACTION7chain 'A' and (resid 645 through 698 )A645 - 698
8X-RAY DIFFRACTION8chain 'A' and (resid 699 through 817 )A699 - 817

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