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- PDB-8w8j: Crystal structure of bacterial prolyl-tRNA synthetase in complex ... -

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Basic information

Entry
Database: PDB / ID: 8w8j
TitleCrystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-19
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: 1.807 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 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 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)130,27621
Polymers128,3902
Non-polymers1,88619
Water13,944774
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint27 kcal/mol
Surface area45040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.668, 102.380, 193.477
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-W1Q / (2~{S})-~{N}-[3-(4-azanyl-5-fluoranyl-quinazolin-7-yl)phenyl]sulfonylpyrrolidine-2-carboxamide


Mass: 415.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18FN5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS, 25% w/v Polyethylene glycol 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: Mar 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.807→96.74 Å / Num. obs: 131943 / % possible obs: 97 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.058 / Net I/σ(I): 19
Reflection shellResolution: 1.807→1.91 Å / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 16048 / CC1/2: 0.873 / Rrim(I) all: 0.459

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.807→96.739 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.179 / SU B: 2.472 / SU ML: 0.075 / Average fsc free: 0.9697 / Average fsc work: 0.9784 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2085 6653 5.046 %
Rwork0.18 125203 -
all0.181 --
obs-131856 96.786 %
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: 25.931 Å2
Baniso -1Baniso -2Baniso -3
1-1.218 Å20 Å20 Å2
2--0.025 Å20 Å2
3----1.243 Å2
Refinement stepCycle: LAST / Resolution: 1.807→96.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8722 0 126 774 9622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129125
X-RAY DIFFRACTIONr_bond_other_d0.0060.0168609
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.6512370
X-RAY DIFFRACTIONr_angle_other_deg0.421.57519801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50351163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.499566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.981101470
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.63110403
X-RAY DIFFRACTIONr_chiral_restr0.0580.21378
X-RAY DIFFRACTIONr_chiral_restr_other0.490.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022043
X-RAY DIFFRACTIONr_nbd_refined0.2060.21641
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.27866
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24452
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24722
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2655
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1350.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.215
X-RAY DIFFRACTIONr_nbd_other0.2640.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.222
X-RAY DIFFRACTIONr_mcbond_it1.7472.7484622
X-RAY DIFFRACTIONr_mcbond_other1.7452.7484622
X-RAY DIFFRACTIONr_mcangle_it2.5234.935795
X-RAY DIFFRACTIONr_mcangle_other2.5234.9315796
X-RAY DIFFRACTIONr_scbond_it2.312.9434503
X-RAY DIFFRACTIONr_scbond_other2.312.9434504
X-RAY DIFFRACTIONr_scangle_it3.6315.36573
X-RAY DIFFRACTIONr_scangle_other3.6315.36574
X-RAY DIFFRACTIONr_lrange_it4.78127.2159990
X-RAY DIFFRACTIONr_lrange_other4.67626.8489805
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
1.807-1.8540.2853570.25971080.26199520.9480.95975.010.233
1.854-1.9050.2674420.23881210.23997240.9560.96588.06050.205
1.905-1.960.2594480.21386670.21594590.960.97196.36330.183
1.96-2.020.2354880.19685610.19892010.9630.97698.3480.167
2.02-2.0860.2144590.18584010.18689040.9710.97999.50580.159
2.086-2.160.2174290.17881590.1886210.970.9899.61720.155
2.16-2.2410.2264400.17778450.17983230.9670.98199.54340.156
2.241-2.3330.2013640.16876610.16980480.9750.98399.71420.149
2.333-2.4360.2113750.16573240.16777110.9730.98499.84440.147
2.436-2.5550.2113570.1770020.17373690.9740.98299.86430.156
2.555-2.6930.2093750.16866560.1770420.9730.98399.84380.156
2.693-2.8560.2033530.16663040.16866600.9750.98399.9550.157
2.856-3.0530.2032660.17259730.17462490.9740.98299.840.169
3.053-3.2980.2123170.18955660.1958910.9730.97999.86420.19
3.298-3.6120.2232680.19351310.19454010.9770.98199.9630.198
3.612-4.0380.1722630.17346550.17349200.9840.98499.95940.185
4.038-4.6610.1582430.14441270.14543730.9850.98999.93140.167
4.661-5.7050.2131870.17835390.1837300.9830.98799.89280.205
5.705-8.0550.2291390.21227860.21329270.9760.9899.93170.238
8.055-96.7390.242830.19716190.19917220.9540.97498.83860.263

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