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- PDB-6q89: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with the ... -

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Basic information

Entry
Database: PDB / ID: 6q89
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Leucyl)-Sulfamoyl)Adenosine
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
Ubiquitin-like (UB roll) - #590 / 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 ...Ubiquitin-like (UB roll) - #590 / 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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
5'-O-(L-leucylsulfamoyl)adenosine / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 / _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)98,7975
Polymers98,1851
Non-polymers6114
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint1 kcal/mol
Surface area37120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.942, 82.935, 228.519
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, 212 molecules

#2: Chemical ChemComp-LSS / 5'-O-(L-leucylsulfamoyl)adenosine / 5-O-N-LEUCYL-SULFAMOYLADENOSINE


Mass: 459.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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.: 208 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
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 1 mM 5'-O-(N-(L-Leucyl)-Sulfamoyl)Adenosine 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: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.09→82.93 Å / Num. obs: 56400 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 43.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Rrim(I) all: 0.087 / Net I/σ(I): 13.8 / Num. measured all: 419417
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.09-2.27.91.13481040.7480.4271.213100
6.6-82.936.50.03120090.9990.0130.03399.7

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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: 2.21→77.96 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.77
RfactorNum. reflection% reflection
Rfree0.2226 2029 4.26 %
Rwork0.1774 --
obs0.1794 47607 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.46 Å2 / Biso mean: 55.2037 Å2 / Biso min: 23.87 Å2
Refinement stepCycle: final / Resolution: 2.21→77.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6486 0 37 208 6731
Biso mean--40.37 50.92 -
Num. residues----852
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.26530.31211430.24331793322100
2.2653-2.32660.3011370.22532473384100
2.3266-2.3950.29521230.2131953318100
2.395-2.47230.25261580.203432323390100
2.4723-2.56070.27541630.200531983361100
2.5607-2.66320.30151360.197532133349100
2.6632-2.78440.27441350.232383373100
2.7844-2.93130.27851460.211532213367100
2.9313-3.11490.26941430.20713216335998
3.1149-3.35540.26351330.200332473380100
3.3554-3.69310.2481310.190532953426100
3.6931-4.22740.18151500.148332953445100
4.2274-5.3260.18021710.143233123483100
5.326-78.00810.17411600.15783490365099
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)
10.79120.5960.59111.02690.25491.06320.1824-0.0269-0.19490.0934-0.06820.04520.18380.0483-0.11160.31570.0043-0.10.35970.01590.39450.7780.3411-30.5003
25.29420.6851.35023.0668-1.04584.554-0.1045-0.4588-0.22940.1292-0.0999-0.0714-0.576-1.04820.17610.40770.1212-0.08560.5506-0.05110.3561-13.763933.8241-14.678
31.004-0.41430.37460.78230.10830.91990.0648-0.0516-0.05170.01980.0501-0.05840.00360.0822-0.10530.2986-0.0122-0.0820.29990.01620.32353.39955.328-28.6324
41.4858-0.0860.90090.4627-0.01021.92880.13280.0314-0.01760.0745-0.00070.0460.0003-0.1826-0.15710.4869-0.0275-0.16640.37950.01650.5637-29.3814-16.6791-54.4494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 250 )A1 - 250
2X-RAY DIFFRACTION2chain 'A' and (resid 251 through 396 )A251 - 396
3X-RAY DIFFRACTION3chain 'A' and (resid 397 through 644 )A397 - 644
4X-RAY DIFFRACTION4chain 'A' and (resid 645 through 875 )A645 - 875

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