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- PDB-7nu1: Crystal Structure of Neisseria gonorrhoeae LeuRS E169G mutant -

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Basic information

Entry
Database: PDB / ID: 7nu1
TitleCrystal Structure of Neisseria gonorrhoeae LeuRS E169G mutant
ComponentsLeucine--tRNA ligase
KeywordsLIGASE / ligand-free structure / Rossmann fold / Leucyl-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 / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Isoleucyl-tRNA Synthetase; Domain 1 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Isoleucyl-tRNA Synthetase; Domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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

Downloads & links

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Assembly

Deposited unit
A: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2033
Polymers98,1131
Non-polymers902
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.049, 81.876, 226.159
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: 98113.281 Da / Num. of mol.: 1 / Fragment: Leucyl-tRNA Synthetase / Mutation: E169G
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.: 115 / 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: 2.31 Å3/Da / Density % sol: 46.85 % / Mosaicity: 0.35 °
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 cryoprotected 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: 0.980114 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980114 Å / Relative weight: 1
ReflectionResolution: 2.51→19.94 Å / Num. obs: 31960 / % possible obs: 99.8 % / Redundancy: 8.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.057 / Rrim(I) all: 0.164 / Net I/σ(I): 9.5 / Num. measured all: 258540 / Scaling rejects: 4
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
2.51-2.658.41.0413835445730.7560.3781.1092.2100
7.95-19.947.20.056763910610.9930.0220.0612593.6

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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: 2.51→19.94 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 1572 4.93 %
Rwork0.2035 30320 -
obs0.2064 31892 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.23 Å2 / Biso mean: 49.385 Å2 / Biso min: 23.8 Å2
Refinement stepCycle: final / Resolution: 2.51→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 2 115 6387
Biso mean--68.48 47.51 -
Num. residues----805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.51-2.590.30771470.246326912838
2.59-2.690.30631330.248626992832
2.69-2.790.30391360.250327162852
2.79-2.920.31261510.242427232874
2.92-3.070.27411350.236327432878
3.07-3.270.30481330.232227402873
3.27-3.520.24071380.211627472885
3.52-3.870.2521370.19727482885
3.87-4.420.26551390.17327882927
4.42-5.550.23091620.177827982960
5.56-19.940.24351610.193729273088
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)
11.57931.17630.74851.53370.3530.81980.05640.1325-0.04440.01350.0092-0.06540.2530.0791-0.05960.30060.0777-0.00810.3075-0.03010.2947-2.4081-11.5161-38.6036
20.19830.06490.00930.85490.05570.39660.03520.0074-0.0218-0-0.04560.027-0.04960.05980.0120.30590.0159-0.02110.411-0.00020.36523.475413.8068-24.7838
32.4092-0.26270.620.9874-0.50212.39030.0301-0.0241-0.1956-0.0790.03050.142-0.0206-0.1074-0.03410.4371-0.00450.01450.35140.00040.382-13.872434.6532-13.5917
40.2105-0.0625-0.11180.92490.01640.6687-0.0203-0.03070.06830.03030.035-0.0259-0.0960.0985-0.02180.3231-0.01430.00170.3131-0.02830.30428.754713.4035-29.4889
52.09920.6039-0.73211.419-0.37771.8799-0.0887-0.4991-0.15840.0413-0.04570.13980.58920.09960.17810.50850.10250.01390.4657-0.00550.3418-13.9476-7.6892-20.3401
61.57790.21840.91111.51220.25152.11780.01040.0649-0.0558-0.14810.00940.28260.0027-0.0603-0.04780.3455-0.0055-0.03450.3512-0.02840.3953-21.2693-17.7877-47.2895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 96 )A1 - 96
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 256 )A97 - 256
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 396 )A257 - 396
4X-RAY DIFFRACTION4chain 'A' and (resid 397 through 564 )A397 - 564
5X-RAY DIFFRACTION5chain 'A' and (resid 565 through 634 )A565 - 634
6X-RAY DIFFRACTION6chain 'A' and (resid 635 through 817 )A635 - 817

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