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- PDB-7nu8: Crystal Structure of Neisseria gonorrhoeae LeuRS in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7nu8
TitleCrystal Structure of Neisseria gonorrhoeae LeuRS 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 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
ADENOSINE-5'-TRIPHOSPHATE / Chem-USB / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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)99,3056
Polymers98,1851
Non-polymers1,1195
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.792, 82.449, 226.974
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 / Fragment: Leucyl-tRNA Synthetase
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

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Non-polymers , 6 types, 206 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-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
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
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 ...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 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: 2.07→77.49 Å / Num. obs: 57375 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.027 / Rrim(I) all: 0.082 / Net I/σ(I): 15.3 / Num. measured all: 530091 / Scaling rejects: 1
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
2.07-2.189.71.1577996982540.740.3891.2221.8100
6.53-77.498.40.0311709620360.9990.0110.03346.999.8

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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: 2.11→56.74 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 2078 3.86 %
Rwork0.1899 51712 -
obs0.1916 53790 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.38 Å2 / Biso mean: 57.2391 Å2 / Biso min: 26.68 Å2
Refinement stepCycle: final / Resolution: 2.11→56.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6608 0 68 201 6877
Biso mean--73.26 51.06 -
Num. residues----870
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.11-2.160.34661480.254333473495
2.16-2.210.3191420.238734043546
2.21-2.270.24811270.221333923519
2.27-2.340.2781250.214234293554
2.34-2.420.25151370.207434163553
2.42-2.50.28971380.205133743512
2.5-2.60.24871370.205834273564
2.6-2.720.24151370.213734343571
2.72-2.860.29351370.218334383575
2.86-3.040.28361390.225534243563
3.04-3.280.28781250.21534603585
3.28-3.610.27121270.200534643591
3.61-4.130.1991460.174434943640
4.13-5.20.20221630.154534993662
5.2-56.740.17961500.168737103860
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)
11.52850.98470.84780.93210.49721.29840.2807-0.0596-0.29280.1603-0.065-0.02810.27310.0246-0.19820.34320.0249-0.10270.33070.00860.36921.2946-3.4532-31.4996
23.33840.16920.34821.6479-0.36346.7032-0.1485-0.5275-0.07090.2375-0.2154-0.4501-0.5435-0.18940.33860.47380.028-0.16360.38870.01990.4413-7.857234.8407-13.4615
31.0638-0.31660.50480.50810.27931.01110.04740.01040.0218-0.07030.033-0.0791-0.09490.008-0.07530.3442-0.0488-0.04150.37630.03540.32441.91813.5617-29.3697
41.5644-0.12280.81630.56640.18711.8680.14-0.0732-0.08970.05720.03420.12450.0394-0.2184-0.19950.4096-0.0325-0.11460.32850.01530.5009-27.023-16.2435-47.2034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 224 )A1 - 224
2X-RAY DIFFRACTION2chain 'A' and (resid 225 through 360 )A225 - 360
3X-RAY DIFFRACTION3chain 'A' and (resid 361 through 583 )A361 - 583
4X-RAY DIFFRACTION4chain 'A' and (resid 584 through 876 )A584 - 876

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