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- PDB-7f96: Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex w... -

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Basic information

Entry
Database: PDB / ID: 7f96
TitlePlasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L95
ComponentsProline--tRNA ligase
KeywordsLIGASE / PROTEIN TRANSLATION / MALARIA / INHIBITOR / PRS
Function / homology
Function and homology information


Ala-tRNA(Pro) deacylase activity / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / ATP binding / cytoplasm
Similarity search - Function
YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II ...YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / 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
Chem-JE6 / PROLINE / Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.577 Å
AuthorsMishra, S. / Malhotra, N. / Yogavel, M. / Sharma, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iscience / Year: 2024
Title: ATP mimetics targeting prolyl-tRNA synthetases as a new avenue for antimalarial drug development
Authors: Mishra, S. / Malhotra, N. / Laleu, B. / Chakraborti, S. / Yogavel, M. / Sharma, A.
History
DepositionJul 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jul 31, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2913
Polymers57,8011
Non-polymers4902
Water1,29772
1
A: Proline--tRNA ligase
hetero molecules

A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5826
Polymers115,6022
Non-polymers9794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4840 Å2
ΔGint-31 kcal/mol
Surface area40250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.610, 103.610, 128.040
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Proline--tRNA ligase / Prolyl-tRNA synthetase / ProRS


Mass: 57801.188 Da / Num. of mol.: 1 / Fragment: UNP residues 254-746
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: proRS, PFL0670c / Plasmid: PETM41 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I5R7, proline-tRNA ligase
#2: Chemical ChemComp-JE6 / ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide


Mass: 374.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
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: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base); BICINE) and 30 % v/v ...Details: 0.2 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base); BICINE) and 30 % v/v Precipitant Mix (40% v/v Ethylene glycol; 20% w/v PEG 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.577→48.542 Å / Num. obs: 25534 / % possible obs: 99.4 % / Redundancy: 19.5 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.084 / Net I/σ(I): 26.1
Reflection shellResolution: 2.58→2.64 Å / Redundancy: 17.1 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1720 / CC1/2: 0.93 / Rrim(I) all: 0.844 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX1.15rc2_3428refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDQ

4ydq


Resolution: 2.577→38.542 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 1273 4.99 %
Rwork0.155 24213 -
obs0.1568 25486 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.82 Å2 / Biso mean: 62.1279 Å2 / Biso min: 29.51 Å2
Refinement stepCycle: final / Resolution: 2.577→38.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 28 72 4036
Biso mean--50.29 58.68 -
Num. residues----488
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.577-2.67970.25641330.1969252595
2.6797-2.80160.26751420.18822684100
2.8016-2.94930.24161400.19272666100
2.9493-3.1340.23251390.17592662100
3.134-3.37590.22821420.17812689100
3.3759-3.71530.21211410.16212689100
3.7153-4.25240.17661430.13822715100
4.2524-5.35520.14981440.12632732100
5.3552-38.540.17411490.15522851100
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)
12.51010.84930.51241.29560.0282.2589-0.0165-0.0220.19690.0573-0.1442-0.01180.02410.19960.08680.44040.01880.02950.4369-0.01840.4155-11.717438.238-14.0804
21.80150.6328-0.01551.20720.01932.04850.0707-0.12620.03870.2062-0.10550.1380.1464-0.04910.09020.42350.00040.02810.3376-0.02610.4119-22.445432.9422-5.9438
31.6816-0.2873-0.61682.5750.6543.3156-0.32420.5134-0.2249-0.9859-0.1968-0.50620.0080.26390.24450.66590.22850.15490.85820.07020.746515.644624.5992-26.2574
41.8482-0.1412-1.10061.55020.13352.2622-0.0079-0.1444-0.00120.142-0.1185-0.21770.11950.4760.12180.44070.0102-0.10790.52950.08460.45671.160535.1887-0.2146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 250 through 338 )A250 - 338
2X-RAY DIFFRACTION2chain 'A' and (resid 339 through 532 )A339 - 532
3X-RAY DIFFRACTION3chain 'A' and (resid 533 through 568 )A533 - 568
4X-RAY DIFFRACTION4chain 'A' and (resid 569 through 746 )A569 - 746

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