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- PDB-7nub: Crystal Structure of Neisseria gonorrhoeae LeuRS L550G mutant in ... -

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Basic information

Entry
Database: PDB / ID: 7nub
TitleCrystal Structure of Neisseria gonorrhoeae LeuRS L550G mutant in Complex with the Reaction Intermediate Leu-AMP
ComponentsLeucine--tRNA ligase
KeywordsLIGASE / Protein-ligand complex / Rossmann fold / Leucyl-tRNA synthetase
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / 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-USB / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 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)98,6794
Polymers98,1291
Non-polymers5503
Water45025
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.309, 81.748, 217.950
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: 98129.242 Da / Num. of mol.: 1 / Fragment: Leucyl-tRNA Synthetase / Mutation: L550G
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-USB / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate


Mass: 460.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N6O8P / 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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.05 % / Mosaicity: 0.08 °
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 5 mM ATP and 5 mM L-leucine 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 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 3.02→108.97 Å / Num. obs: 17973 / % possible obs: 98.9 % / Redundancy: 12.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.07 / Rrim(I) all: 0.247 / Net I/σ(I): 12 / Num. measured all: 220750 / Scaling rejects: 50
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
3.02-3.1813.31.523435425820.7650.4321.5812.7100
9.54-108.9711.30.06276486760.9990.0190.06529.899.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q89

6q89


Resolution: 3.02→65.39 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 912 5.09 %
Rwork0.2207 16998 -
obs0.224 17910 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 243.13 Å2 / Biso mean: 72.5075 Å2 / Biso min: 21.11 Å2
Refinement stepCycle: final / Resolution: 3.02→65.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5888 0 33 25 5946
Biso mean--45.72 46.37 -
Num. residues----773
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.02-3.180.38571400.270323822522100
3.18-3.380.34481390.253823982537100
3.38-3.640.2751240.229324102534100
3.64-40.28221210.1962247236892
4-4.580.25871340.18524492583100
4.58-5.770.2641120.210824922604100
5.77-65.390.2871420.242626202762100
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)
12.0050.94381.04221.27170.66461.58320.07420.0815-0.10450.09360.0484-0.01590.14650.2013-0.13390.35770.0561-0.03550.4135-0.02830.40030.4655-1.7054-30.2108
21.29180.4178-1.1291.7594-0.0461.28390.3398-1.52820.25940.3816-0.44120.1656-0.16270.40580.1061.2596-0.1080.03541.5294-0.15491.0119-9.051241.2851-12.0629
31.4282-0.16720.78772.1726-0.17481.0801-0.22930.06620.4581-0.10460.1307-0.1177-0.42090.05690.16090.611-0.0712-0.0840.52270.07550.52372.236222.7832-25.8381
41.66050.76541.11051.13090.69011.27110.13150.1427-0.14860.0906-0.01830.03940.21290.11-0.1080.38760.0421-0.04410.4014-0.05790.388-10.1226-11.7491-38.6022
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 386 )A236 - 386
3X-RAY DIFFRACTION3chain 'A' and (resid 387 through 466 )A387 - 466
4X-RAY DIFFRACTION4chain 'A' and (resid 467 through 815 )A467 - 815

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