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- PDB-8w9i: Crystal structure of bacterial prolyl-tRNA synthetase in complex ... -

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Basic information

Entry
Database: PDB / ID: 8w9i
TitleCrystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-5
ComponentsProline--tRNA ligase
KeywordsLIGASE / Inhibitor
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / cytosol
Similarity search - Function
Prolyl-tRNA synthetase, class IIa, type 1 / Prolyl-tRNA synthetase, class IIa, bacterial-type / Prokaryote proline-tRNA ligase core domain / Proline--tRNA ligase, anticodon binding domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / : / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) ...Prolyl-tRNA synthetase, class IIa, type 1 / Prolyl-tRNA synthetase, class IIa, bacterial-type / Prokaryote proline-tRNA ligase core domain / Proline--tRNA ligase, anticodon binding domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / : / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
: / Proline--tRNA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLuo, Z. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22207133 China
National Natural Science Foundation of China (NSFC)22177140 China
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Development of potent inhibitors targeting bacterial prolyl-tRNA synthetase through fluorine scanning-directed activity tuning.
Authors: Luo, Z. / Qiu, H. / Peng, X. / Tan, Q. / Chen, B. / Gu, Q. / Liu, H. / Zhou, H.
History
DepositionSep 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proline--tRNA ligase
B: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,63013
Polymers128,3902
Non-polymers1,24011
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-31 kcal/mol
Surface area45010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.584, 102.622, 194.084
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 Proline--tRNA ligase


Mass: 64194.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: proS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I502
#2: Chemical ChemComp-W2H / (2~{S})-~{N}-[3-(4-azanylquinazolin-7-yl)phenyl]sulfonylpyrrolidine-2-carboxamide


Mass: 397.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M BIS-TRIS, 26% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.35→97.05 Å / Num. obs: 55512 / % possible obs: 99 % / Redundancy: 6.4 % / CC1/2: 0.963 / Rmerge(I) obs: 0.126 / Net I/σ(I): 12.6
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.911 / Num. unique obs: 5949 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-3000data scaling
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→49.656 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.2 / SU B: 9.114 / SU ML: 0.202 / Average fsc free: 0.9536 / Average fsc work: 0.966 / Cross valid method: FREE R-VALUE / ESU R: 0.383 / ESU R Free: 0.254
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2484 2791 5.028 %
Rwork0.2141 52721 -
all0.216 --
obs-55512 99.795 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.717 Å2
Baniso -1Baniso -2Baniso -3
1-1.739 Å2-0 Å20 Å2
2---1.726 Å2-0 Å2
3----0.012 Å2
Refinement stepCycle: LAST / Resolution: 2.45→49.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8652 0 83 138 8873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0128900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168423
X-RAY DIFFRACTIONr_angle_refined_deg0.8111.64712066
X-RAY DIFFRACTIONr_angle_other_deg0.2891.57419352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34951133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.364565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.739101423
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.87410379
X-RAY DIFFRACTIONr_chiral_restr0.0380.21359
X-RAY DIFFRACTIONr_chiral_restr_other0.0060.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210757
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021987
X-RAY DIFFRACTIONr_nbd_refined0.1860.21601
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.27694
X-RAY DIFFRACTIONr_nbtor_refined0.1670.24312
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.24571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0780.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1070.28
X-RAY DIFFRACTIONr_nbd_other0.1660.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0760.23
X-RAY DIFFRACTIONr_mcbond_it1.2584.2054541
X-RAY DIFFRACTIONr_mcbond_other1.2574.2054541
X-RAY DIFFRACTIONr_mcangle_it2.1667.5575671
X-RAY DIFFRACTIONr_mcangle_other2.1667.5585672
X-RAY DIFFRACTIONr_scbond_it1.1314.1854359
X-RAY DIFFRACTIONr_scbond_other1.1314.1854360
X-RAY DIFFRACTIONr_scangle_it2.0027.6886395
X-RAY DIFFRACTIONr_scangle_other2.0027.6896396
X-RAY DIFFRACTIONr_lrange_it3.39938.179290
X-RAY DIFFRACTIONr_lrange_other3.39938.1719291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.45-2.5130.3571900.29838540.30140510.9260.94199.82720.279
2.513-2.5820.2841820.2737640.27139530.9430.95399.82290.248
2.582-2.6570.311790.26836550.2738400.9330.95499.84380.242
2.657-2.7380.2862100.25535080.25737210.9490.95999.91940.226
2.738-2.8280.3191730.24434470.24836280.9340.96299.77950.217
2.828-2.9270.2942060.23932990.24235080.9440.96399.91450.21
2.927-3.0370.2451600.22432150.22533760.9610.96899.97040.197
3.037-3.160.2451760.21930920.2232680.960.9691000.198
3.16-3.30.2661570.22129790.22331380.9530.96999.93630.201
3.3-3.4610.2651500.22128530.22330030.9590.9711000.205
3.461-3.6470.2591390.2127360.21228750.9590.9751000.197
3.647-3.8670.2071350.19325770.19427130.9740.97999.96310.182
3.867-4.1320.211140.17824620.17925780.9760.98299.92240.169
4.132-4.460.1931230.16322670.16423910.9780.98499.95820.156
4.46-4.8820.1911030.15421210.15622270.9790.98599.86530.151
4.882-5.4520.2291230.18818770.1920010.970.9899.950.188
5.452-6.2830.247850.2217260.22118120.9730.97499.94480.215
6.283-7.6640.282800.22714480.2315300.9360.96799.86930.226
7.664-10.7120.236650.20211610.20412360.960.96999.19090.22
10.712-49.6560.262400.3416700.3367560.9490.92493.91530.375

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