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- PDB-6q8c: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with 5'-O... -

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Basic information

Entry
Database: PDB / ID: 6q8c
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with 5'-O-(N-(L-Leucyl)-Sulfamoyl)Uridine
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
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
5'-O-(N-(L-Leucyl)-Sulfamoyl)Uridine / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsPang, L. / De Graef, S. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - FlandersG077814N Belgium
Research Foundation - FlandersG0A4616N Belgium
Research Foundation - Flanders1109117N Belgium
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases.
Authors: Nautiyal, M. / De Graef, S. / Pang, L. / Gadakh, B. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2019Group: Data collection / Category: pdbx_database_proc
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)98,8366
Polymers98,1851
Non-polymers6505
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint3 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.321, 82.001, 227.725
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, WHOK_00006, WHOM_00006, WHOO_00006, WHOP_00006, WHOU_00006, WHOW_00006, WHOX_00006, WHOY_00006, WHOZ_00006
Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS / References: UniProt: A0A1D3HNX6, leucine-tRNA ligase

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Non-polymers , 5 types, 195 molecules

#2: Chemical ChemComp-LSU / 5'-O-(N-(L-Leucyl)-Sulfamoyl)Uridine


Mass: 436.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N4O9S / 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


Mass: 62.068 Da / Num. of mol.: 2 / 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.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.55 %
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 5'-O-(N-(L-Leucyl)-Sulfamoyl)Uridine in an equivalent 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: 0.979965 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979965 Å / Relative weight: 1
ReflectionResolution: 2.15→227.73 Å / Num. obs: 51166 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 47.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.036 / Rrim(I) all: 0.104 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.278.41.19973410.7080.4381.278100
6.81-227.737.60.03918210.9990.0150.04299.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A model generated from 3ZJU

3zju


Resolution: 2.31→113.862 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.87
RfactorNum. reflection% reflection
Rfree0.2509 2094 5.03 %
Rwork0.1997 --
obs0.2023 41601 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.06 Å2 / Biso mean: 62.7475 Å2 / Biso min: 30.18 Å2
Refinement stepCycle: final / Resolution: 2.31→113.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6303 0 39 190 6532
Biso mean--50.94 53.97 -
Num. residues----832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.31-2.36380.3091210.230126292750
2.3638-2.42290.31741410.239525822723
2.4229-2.48840.29221200.242426102730
2.4884-2.56160.30511410.242925972738
2.5616-2.64430.28351730.230625512724
2.6443-2.73880.33381480.239626262774
2.7388-2.84850.26741300.223825622692
2.8485-2.97810.30791370.225826142751
2.9781-3.13520.29161300.219426202750
3.1352-3.33160.25571420.224326182760
3.3316-3.58880.26511370.207426402777
3.5888-3.950.24751350.181626462781
3.95-4.52160.20111660.168526532819
4.5216-5.69680.25861330.170726982831
5.6968-114.0010.20671400.194728613001
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)
12.57242.36282.01541.90851.71291.93680.47610.2457-0.59110.35150.0597-0.46340.7850.3692-0.46450.53030.0841-0.2450.5211-0.10150.62151.0347-11.4801-36.4763
20.9296-0.2720.61651.1230.15742.0316-0.115-0.07730.27810.0982-0.16480.2921-0.4524-0.07560.2470.413-0.0665-0.07720.4769-0.02860.48580.135320.5624-21.7372
32.80571.69050.27711.341-0.96566.2233-0.4104-0.4389-0.16350.4835-0.3805-0.6341-1.3042-0.31910.69680.7390.138-0.32080.5804-0.02390.7561-10.16233.4676-11.4901
43.5093-1.61741.12821.7208-0.14691.8851-0.1449-0.19130.2398-0.01890.131-0.0104-0.2995-0.18080.01590.4121-0.0702-0.12270.434-0.01730.3888-0.988421.2864-24.0331
52.86470.49880.16550.52020.44620.27650.03590.2915-0.3110.07420.0169-0.04630.12660.1941-0.02320.37310.029-0.10430.4013-0.05220.4877-1.0084-1.5977-31.1469
62.64091.41612.42421.81432.20494.2070.2890.0177-0.05180.2497-0.11040.09220.3974-0.0534-0.1720.4968-0.0159-0.18370.4023-0.01330.5185-21.9539-20.7305-48.9401
75.3535-4.3682-0.22565.7715-0.31863.2099-0.07031.30970.38550.267-0.04510.9182-0.7325-0.62860.16390.95650.103-0.16450.78560.11810.893-48.997-2.6379-68.9821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 146 )A1 - 146
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 256 )A147 - 256
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 361 )A257 - 361
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 489 )A362 - 489
5X-RAY DIFFRACTION5chain 'A' and (resid 490 through 644 )A490 - 644
6X-RAY DIFFRACTION6chain 'A' and (resid 645 through 808 )A645 - 808
7X-RAY DIFFRACTION7chain 'A' and (resid 809 through 875 )A809 - 875

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