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- PDB-6q8a: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with 5'-O... -

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Basic information

Entry
Database: PDB / ID: 6q8a
TitleNeisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with 5'-O-(N-(L-Leucyl)-Sulfamoyl)Cytidine
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 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
5'-O-(N-(L-Leucyl)-Sulfamoyl)Cytidine / Leucine--tRNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsPang, L. / De Graef, S. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - FlandersG077814N Belgium
Research Foundation - FlandersG0A4616N Belgium
Research Foundation - Flanders1109117N Belgium
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases.
Authors: Nautiyal, M. / De Graef, S. / Pang, L. / Gadakh, B. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2019Group: Data collection / Category: pdbx_database_proc
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)98,7114
Polymers98,1851
Non-polymers5253
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-3 kcal/mol
Surface area36360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.151, 81.695, 225.429
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: 98185.344 Da / Num. of mol.: 1 / Fragment: Leucyl-tRNA Synthetase / Mutation: D454N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria)
Strain: NCCP11945 / Gene: leuS, NGK_0009 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS / References: UniProt: B4RNT1, leucine-tRNA ligase
#2: Chemical ChemComp-HQ5 / 5'-O-(N-(L-Leucyl)-Sulfamoyl)Cytidine


Mass: 435.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N5O8S / 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.: 269 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.63 %
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 5'-O-(N-(L-Leucyl)-Sulfamoyl)Cytidine iin 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: ID23-1 / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.09→112.71 Å / Num. obs: 53482 / % possible obs: 97.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 37.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.033 / Rrim(I) all: 0.083 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.09-2.24.80.59670110.7240.290.66789
6.61-112.715.70.04819220.9970.0210.05298.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A model generated from 3ZJU

3zju


Resolution: 2.11→112.71 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.24
RfactorNum. reflection% reflection
Rfree0.2473 2075 3.98 %
Rwork0.1999 --
obs0.2019 52071 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.42 Å2 / Biso mean: 43.715 Å2 / Biso min: 20.55 Å2
Refinement stepCycle: final / Resolution: 2.11→112.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6327 0 31 271 6629
Biso mean--32.98 44.06 -
Num. residues----820
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 (%)
2.11-2.15910.2941910.24683021311288
2.1591-2.21310.34031160.24713058317491
2.2131-2.27290.28411220.23793162328494
2.2729-2.33980.3091340.22093260339496
2.3398-2.41530.28751360.21693287342399
2.4153-2.50170.26141570.211733733530100
2.5017-2.60190.28661540.216333893543100
2.6019-2.72030.30561410.216633993540100
2.7203-2.86370.27981370.219133433480100
2.8637-3.04310.27811400.22373380352098
3.0431-3.27810.2611380.213934393577100
3.2781-3.6080.2591760.199333493525100
3.608-4.13010.21751440.181234673611100
4.1301-5.20360.20381440.173422356698
5.2036-112.87560.20851450.18943647379299
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)
11.35290.92750.96991.24330.96790.83080.11740.0852-0.20960.0729-0.0373-0.0710.22790.0755-0.07290.28860.0349-0.02720.3146-0.02050.33332.3702-6.7541-34.793
20.3609-0.2456-0.24860.55490.28771.8480.0858-0.06370.07920.0177-0.12970.0789-0.20530.0440.02040.2807-0.0472-0.03310.30370.01260.383-1.326823.1777-21.1745
30.768-0.698-0.19151.14770.20230.76160.1074-0.0630.0361-0.06360.02030.0561-0.20550.0112-0.12280.3691-0.0429-0.01870.31230.02410.3448-4.803428.133-17.7804
41.69780.29730.10240.56330.21540.3992-0.0062-0.144-0.05360.1357-0.0153-0.00860.15390.07850.01670.29270.0384-0.02560.2842-0.00160.251-4.2265-2.1145-29.7959
52.59410.99721.40872.05240.8155.40990.12720.05970.0416-0.222-0.02370.16160.1436-0.0635-0.07950.19470.0092-0.05440.1984-0.05030.3218-25.6155-18.9655-52.0991
61.0402-1.19520.88131.8221-0.26631.9696-0.06110.4321-0.0311-0.15080.02950.4576-0.36050.3822-0.06780.4172-0.0515-0.13340.2761-0.0080.5015-26.2452-12.4262-58.2546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 159 )A1 - 159
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 256 )A160 - 256
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 489 )A257 - 489
4X-RAY DIFFRACTION4chain 'A' and (resid 490 through 674 )A490 - 674
5X-RAY DIFFRACTION5chain 'A' and (resid 675 through 778 )A675 - 778
6X-RAY DIFFRACTION6chain 'A' and (resid 779 through 875 )A779 - 875

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