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- PDB-7nty: Crystal Structure of Neisseria gonorrhoeae LeuRS L550A mutant -

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Basic information

Entry
Database: PDB / ID: 7nty
TitleCrystal Structure of Neisseria gonorrhoeae LeuRS L550A mutant
ComponentsLeucine--tRNA ligase
KeywordsLIGASE / ligand-free protein / 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 / 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
Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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: Commun Biol / Year: 2022
Title: Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip.
Authors: Pang, L. / Zanki, V. / Strelkov, S.V. / Van Aerschot, A. / Gruic-Sovulj, I. / Weeks, S.D.
History
DepositionMar 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2333
Polymers98,1431
Non-polymers902
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.072, 81.680, 226.968
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 98143.266 Da / Num. of mol.: 1 / Fragment: Leucyl-tRNA Synthetase / Mutation: L550A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: NCCP11945 / Gene: leuS, NGK_0009 / Plasmid: pETRUK / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS / References: UniProt: B4RNT1, leucine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
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 8.0, 0.1 M MgCl2, 20% (w/v) PEG 3350 and a crystal seed stock in a ...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 8.0, 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 cryo-protected 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: 2.37→76.85 Å / Num. obs: 38322 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.039 / Rrim(I) all: 0.141 / Net I/σ(I): 14.6 / Num. measured all: 500026 / Scaling rejects: 7
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
2.37-2.4913.11.3647180854760.7290.3891.421.9100
7.48-76.85120.0441661113810.9990.0130.0464299.9

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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: 2.39→56.74 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 1830 4.93 %
Rwork0.1957 35323 -
obs0.1983 37153 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.8 Å2 / Biso mean: 57.2887 Å2 / Biso min: 29.44 Å2
Refinement stepCycle: final / Resolution: 2.39→56.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6218 0 2 122 6342
Biso mean--94.34 52.85 -
Num. residues----802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.39-2.450.35671460.286326842830
2.45-2.530.35051330.275526272760
2.53-2.610.33041320.253926912823
2.61-2.70.29761530.237626582811
2.7-2.810.30551380.229726772815
2.81-2.940.30621330.222926952828
2.94-3.090.2591480.215726922840
3.09-3.290.25891260.216927372863
3.29-3.540.27081490.20326832832
3.54-3.90.24871300.183527212851
3.9-4.460.21471480.162227472895
4.46-5.620.20781470.164627742921
5.62-56.740.21291470.184529373084
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)
11.89211.37551.08151.82491.30841.41130.12090.1873-0.3070.13590.0947-0.14850.27570.1592-0.19880.38480.0661-0.08210.3937-0.01360.40381.7078-9.719-36.7655
20.3827-0.2934-0.18710.8469-0.09271.39030.1124-0.05420.1088-0.0342-0.04490.1624-0.04770.1363-0.06510.3951-0.0517-0.03960.4264-0.00950.5170.501222.0085-20.9195
35.0301-0.26531.70842.8874-0.96566.09090.0985-0.0539-0.1189-0.18550.00730.2388-0.1908-0.1785-0.13430.3788-0.0094-0.00130.2806-0.0180.4511-14.041934.3639-13.4128
40.66840.0308-0.18940.92280.14981.00030.0098-0.02290.09450.06870.0927-0.0845-0.08820.081-0.11720.3998-0.0026-0.04510.4011-0.02850.36418.531612.6731-29.7781
52.45790.2963-0.2151.03640.37360.10630.2464-0.5088-0.250.5726-0.06810.32080.10070.0992-0.10470.7137-0.0416-0.03810.52890.02980.3801-13.1607-9.8495-22.0192
62.52120.80672.08022.15430.93124.2330.07960.0725-0.0065-0.2239-0.13370.33710.1688-0.19440.03090.41320.0015-0.090.342-0.0680.4613-22.7454-18.2208-50.4208
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 396 )A257 - 396
4X-RAY DIFFRACTION4chain 'A' and (resid 397 through 565 )A397 - 565
5X-RAY DIFFRACTION5chain 'A' and (resid 566 through 653 )A566 - 653
6X-RAY DIFFRACTION6chain 'A' and (resid 654 through 817 )A654 - 817

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