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- PDB-7ap2: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Comp... -

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Basic information

Entry
Database: PDB / ID: 7ap2
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound LeuS7HMDDA
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 / cytoplasm / cytosol
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-RRW / Leucine--tRNA ligase / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPang, L. / De Graef, S. / 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: Molecules / Year: 2020
Title: Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors.
Authors: Zhang, B. / Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Lescrinier, E. / Rozenski, J. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionOct 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)98,8876
Polymers98,1851
Non-polymers7015
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint6 kcal/mol
Surface area36750 Å2
Unit cell
Length a, b, c (Å)49.237, 80.987, 224.983
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) / Strain (production host): Rosetta 2 (DE3) pLysS
References: UniProt: A0A5K1KQ39, UniProt: Q5FAJ3*PLUS, leucine-tRNA ligase

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Non-polymers , 5 types, 218 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-RRW / [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate


Mass: 487.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H29N5O8S / Feature type: SUBJECT OF INVESTIGATION
#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.: 213 / 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: 2.28 Å3/Da / Density % sol: 46.15 % / Mosaicity: 0.23 °
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 LeuS7HMDDA 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: 0.979997 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979997 Å / Relative weight: 1
ReflectionResolution: 2.22→112.49 Å / Num. obs: 45493 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.049 / Rrim(I) all: 0.175 / Net I/σ(I): 10.6 / Num. measured all: 587009 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.22-2.3413.11.3878564065450.7210.3981.4442
7.03-112.4911.90.0591938416230.9990.0170.06229

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q89

6q89


Resolution: 2.25→56.25 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 2006 4.58 %
Rwork0.1875 41747 -
obs0.1897 43753 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.27 Å2 / Biso mean: 49.5062 Å2 / Biso min: 24.7 Å2
Refinement stepCycle: final / Resolution: 2.25→56.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 43 213 6724
Biso mean--39.19 45.51 -
Num. residues----843
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.25-2.310.35731380.288829053043
2.31-2.370.34341400.263929503090
2.37-2.440.30611450.247829163061
2.44-2.520.3141550.236829213076
2.52-2.610.26341520.221129463098
2.61-2.710.25911230.218529693092
2.71-2.830.29571400.213329333073
2.83-2.980.27441540.215629463100
2.98-3.170.29621430.198429733116
3.17-3.420.25481440.192529713115
3.42-3.760.20611300.169830303160
3.76-4.30.18771450.153630073152
4.3-5.420.16721500.157630593209
5.42-56.250.22471470.174532213368
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)
10.25040.19590.23020.6540.52750.63030.04440.0707-0.09870.07010.04180.01930.12010.0875-0.08820.30240.0122-0.03460.3724-0.01610.36591.12630.9378-31.135
23.778-0.20210.51310.4451-0.70564.25270.061-0.0533-0.23310.0580.01220.0192-0.20990.2026-0.06410.43960.00520.00370.2946-0.02770.455-8.370235.3607-11.1201
30.2723-0.0061-0.15490.45250.20860.64790.02310.01560.0828-0.03980.010.0007-0.05140.0471-0.0380.2894-0.0102-0.02870.32370.01510.3412.475317.0177-27.9684
43.33351.0892-1.40762.2576-1.48863.5920.0091-0.3608-0.18210.5110.15270.19920.2435-0.3328-0.05620.51560.0314-0.01580.364-0.07020.3582-14.0323-7.5833-20.975
51.40050.42671.12841.61821.00363.97640.1058-0.06590.00520.0848-0.04540.20480.0931-0.1567-0.05580.262-0.0070.01710.252-0.03770.3528-22.6044-17.2248-44.9641
63.1532-0.28921.09240.9801-0.35781.654-0.13270.69390.2735-0.23-0.02940.2524-0.4248-0.00640.03280.54650.0433-0.15110.52910.00020.4698-31.1479-9.1981-60.8346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 235 )A1 - 235
2X-RAY DIFFRACTION2chain 'A' and (resid 236 through 361 )A236 - 361
3X-RAY DIFFRACTION3chain 'A' and (resid 362 through 564 )A362 - 564
4X-RAY DIFFRACTION4chain 'A' and (resid 565 through 631 )A565 - 631
5X-RAY DIFFRACTION5chain 'A' and (resid 632 through 780 )A632 - 780
6X-RAY DIFFRACTION6chain 'A' and (resid 781 through 875 )A781 - 875

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