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- PDB-7ntz: Crystal Structure of Neisseria gonorrhoeae LeuRS L550A mutant in ... -

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Basic information

Entry
Database: PDB / ID: 7ntz
TitleCrystal Structure of Neisseria gonorrhoeae LeuRS L550A mutant in Complex with the Reaction Intermediate Leu-AMP
ComponentsLeucine--tRNA ligase
KeywordsLIGASE / protein-ligand 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 / 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-USB / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)98,6934
Polymers98,1431
Non-polymers5503
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.935, 81.446, 217.410
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-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


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
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 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 8.0, 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 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 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: 2.05→108.71 Å / Num. obs: 55849 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.03 / Rrim(I) all: 0.093 / Net I/σ(I): 14.1 / Num. measured all: 522825 / Scaling rejects: 6
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
2.05-2.169.71.2217771380130.7010.4121.291.7100
6.48-108.718.70.0331725319850.9990.0110.03546.799.8

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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: 2.1→54.35 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1917 3.7 %
Rwork0.2015 49893 -
obs0.2025 51810 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.81 Å2 / Biso mean: 55.267 Å2 / Biso min: 26.28 Å2
Refinement stepCycle: final / Resolution: 2.1→54.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5971 0 33 213 6217
Biso mean--38.08 51.16 -
Num. residues----776
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
2.1-2.150.30921370.246835093646
2.15-2.210.28621670.23434973664
2.21-2.280.2951530.220634553608
2.28-2.350.26981430.212334943637
2.35-2.430.23151180.210635763694
2.43-2.530.23571130.202235053618
2.53-2.650.2271220.201435553677
2.65-2.790.25181470.196435273674
2.79-2.960.26251220.206435583680
2.96-3.190.28461230.205735743697
3.19-3.510.22471390.205235973736
3.51-4.020.18731290.18435973726
4.02-5.060.19471450.179136413786
5.06-54.350.23091590.218538083967
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)
11.5231.01970.90411.27310.76361.21250.12260.0782-0.19430.1610.0124-0.13070.18460.035-0.15260.34450.0379-0.06980.3517-0.03820.35651.8792-4.7316-30.2719
20.4773-0.1552-0.03514.0271.25550.7536-0.1109-0.31660.32160.32270.03630.3557-0.47120.04280.07380.70740.0073-0.0060.6834-0.02120.5821-8.202936.1041-18.0679
31.3850.61660.6980.96190.53260.77220.10070.0932-0.15940.0886-0.0051-0.03970.14790.1033-0.10040.33590.0243-0.04930.3342-0.0240.3113-7.4236-10.1717-37.2143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 208 )A1 - 208
2X-RAY DIFFRACTION2chain 'A' and (resid 209 through 437 )A209 - 437
3X-RAY DIFFRACTION3chain 'A' and (resid 438 through 816 )A438 - 816

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