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- PDB-7yp8: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Leuc... -

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Basic information

Entry
Database: PDB / ID: 7yp8
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Leucyl-sulfamoyl 3-deazaadenosine
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 / 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: 2.1 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)G0A4616N Belgium
Research Foundation - Flanders (FWO)1S53516N Belgium
CitationJournal: To be published
Title: The essential role of a structured water in base recognition of Class II aminoacyl-tRNA synthetases
Authors: Pang, L. / De Graef, S. / Zhang, B. / Strelkov, S.V. / Van Aerschot, A. / Weeks, S.D.
History
DepositionAug 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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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)98,7965
Polymers98,1851
Non-polymers6104
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-3 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.794, 82.979, 229.250
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 / Mutation: D454N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria)
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

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Non-polymers , 5 types, 329 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-JIE / [(2R,3S,4R,5R)-5-(4-azanylimidazo[4,5-c]pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl N-[(2S)-2-azanyl-4-methyl-pentanoyl]sulfamate


Mass: 458.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H26N6O7S / 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.: 325 / 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: 2.36 Å3/Da / Density % sol: 47.96 % / Mosaicity: 0.22 °
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 inhibitor 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: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.09→82.98 Å / Num. obs: 56718 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.034 / Rrim(I) all: 0.094 / Net I/σ(I): 12.9 / Num. measured all: 424072 / Scaling rejects: 5
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
2.09-2.27.90.956473281550.7510.3571.0162.1100
6.59-82.986.70.0461342420120.9980.0180.04932.599.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q89

6q89


Resolution: 2.1→56.21 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 2159 3.89 %
Rwork0.1794 53286 -
obs0.1814 55445 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.75 Å2 / Biso mean: 52.716 Å2 / Biso min: 25.98 Å2
Refinement stepCycle: final / Resolution: 2.1→56.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 37 325 6958
Biso mean--39.33 51.29 -
Num. residues----866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.28981350.248935013636100
2.15-2.20.26081340.220535063640100
2.2-2.260.24371580.21534643622100
2.26-2.330.24811490.200535353684100
2.33-2.40.26861340.197734843618100
2.4-2.490.26551450.200435063651100
2.49-2.590.26011370.201435633700100
2.59-2.710.28221340.200935313665100
2.71-2.850.23431390.200835223661100
2.85-3.030.27151680.210835113679100
3.03-3.260.28721450.19835543699100
3.26-3.590.25221420.187635623704100
3.59-4.110.19311480.161336053753100
4.11-5.180.20341500.145736183768100
5.18-56.210.18791410.16153824396599
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)
10.82490.42030.43631.12880.33831.12450.189-0.0387-0.21860.0721-0.0459-0.00840.22520.0454-0.13920.29630.0083-0.10640.31910.01640.32020.7176-1.9212-31.4868
22.63450.70110.0212.7205-0.71053.8009-0.0443-0.4656-0.15810.0856-0.1462-0.1623-0.5741-0.69670.18790.47870.1097-0.10950.5317-0.02590.3784-12.27835.0563-14.4867
30.55780.07740.34440.32080.16930.73330.11650.0103-0.1338-0.00280.01380.0660.0915-0.0517-0.13920.36560.0113-0.11270.3450.0360.4036-13.0582-5.8581-40.7923
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 396 )A236 - 396
3X-RAY DIFFRACTION3chain 'A' and (resid 397 through 875 )A397 - 875

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