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- PDB-8w8l: Crystal structure of bacterial prolyl-tRNA synthetase in complex ... -

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Basic information

Entry
Database: PDB / ID: 8w8l
TitleCrystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-38
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 148 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.824 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: To Be Published
Title: Structure-Guided Fluorine Scanning Accelerates the Discovery of Potent and Selective Inhibitors Against Bacterial Prolyl-tRNA Synthetase
Authors: Luo, Z. / Zhou, H.
History
DepositionSep 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 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: Proline--tRNA ligase
B: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,50828
Polymers128,3902
Non-polymers2,11926
Water14,538807
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-94 kcal/mol
Surface area44810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.484, 103.060, 194.095
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, 2 molecules AB

#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 148 (bacteria) / Gene: proS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I502

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Non-polymers , 5 types, 833 molecules

#2: Chemical ChemComp-W20 / (2~{S})-~{N}-[5-(4-azanyl-8-fluoranyl-quinazolin-7-yl)-2-fluoranyl-phenyl]sulfonylpyrrolidine-2-carboxamide


Mass: 433.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17F2N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
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: 0.9785 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: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.82→97.05 Å / Num. obs: 132338 / % possible obs: 99.1 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Net I/σ(I): 20.3
Reflection shellResolution: 1.82→1.92 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 18059 / CC1/2: 0.866 / Rrim(I) all: 0.51

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.824→97.048 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.892 / SU ML: 0.112 / Cross valid method: FREE R-VALUE / ESU R: 0.131 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2412 6624 5.009 %
Rwork0.2112 125617 -
all0.213 --
obs-132241 99.022 %
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: 25.033 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2---1.029 Å2-0 Å2
3----1.061 Å2
Refinement stepCycle: LAST / Resolution: 1.824→97.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8681 0 132 807 9620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0129057
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168562
X-RAY DIFFRACTIONr_angle_refined_deg1.0471.64912287
X-RAY DIFFRACTIONr_angle_other_deg0.3761.57519697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47351156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.049566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.588101461
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.27810391
X-RAY DIFFRACTIONr_chiral_restr0.0490.21377
X-RAY DIFFRACTIONr_chiral_restr_other0.0720.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022018
X-RAY DIFFRACTIONr_nbd_refined0.1970.21770
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.28177
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24427
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24730
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2671
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.030.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.090.28
X-RAY DIFFRACTIONr_nbd_other0.1830.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.220
X-RAY DIFFRACTIONr_mcbond_it1.0322.7374585
X-RAY DIFFRACTIONr_mcbond_other1.0312.7374585
X-RAY DIFFRACTIONr_mcangle_it1.7254.9155742
X-RAY DIFFRACTIONr_mcangle_other1.7254.9165743
X-RAY DIFFRACTIONr_scbond_it1.1042.8054472
X-RAY DIFFRACTIONr_scbond_other1.1042.8054473
X-RAY DIFFRACTIONr_scangle_it1.8575.1136541
X-RAY DIFFRACTIONr_scangle_other1.8575.1136542
X-RAY DIFFRACTIONr_lrange_it3.5126.17710064
X-RAY DIFFRACTIONr_lrange_other3.39325.6069882
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
1.824-1.8710.3244330.31684060.31697960.910.91590.23070.282
1.871-1.9220.3164850.2987260.29195060.9050.92596.89670.256
1.922-1.9780.2954560.26987780.2792390.9230.93499.94590.232
1.978-2.0390.2894700.26185530.26290240.9240.94199.98890.224
2.039-2.1060.2514330.24583020.24687380.9440.9599.96570.213
2.106-2.180.3094210.24380280.24784520.9240.95199.96450.214
2.18-2.2620.2573710.22778070.22881810.9480.95999.96330.201
2.262-2.3540.2553920.22274780.22478710.9490.96299.98730.197
2.354-2.4590.2533440.21372110.21575590.9530.96699.94710.192
2.459-2.5790.2533680.21468920.21672610.950.96699.98620.197
2.579-2.7180.2453760.20964790.21168570.960.96899.97080.193
2.718-2.8830.2233210.20262210.20365430.9610.97199.98470.191
2.883-3.0820.2463070.20158350.20461480.9580.97299.90240.195
3.082-3.3280.2482790.21354620.21557440.9570.97199.94780.211
3.328-3.6450.2113030.20950000.20953040.9740.97599.98110.212
3.645-4.0750.222740.18245430.18448200.9670.97999.93780.192
4.075-4.7040.1891970.15440920.15542930.9810.98599.90680.171
4.704-5.7580.2261550.17734860.17936420.9720.98599.97250.197
5.758-8.1290.2391500.20927270.2128780.9730.9899.96530.229
8.129-97.0480.191890.20415910.20316910.9830.97199.34950.258

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