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- PDB-7f97: Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex w... -

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Basic information

Entry
Database: PDB / ID: 7f97
TitlePlasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L97
ComponentsProline--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / MALARIA / INHIBITOR / PRS / LIGASE / LIGASE-LIGASE INHIBITOR complex
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-1XK / 1,4-BUTANEDIOL / HEXANE-1,6-DIOL / PROLINE / Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsMishra, S. / Malhotra, N. / Yogavel, M. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
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
B: Proline--tRNA ligase
C: Proline--tRNA ligase
D: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,13824
Polymers231,2054
Non-polymers2,93320
Water1,00956
1
A: Proline--tRNA ligase
B: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,09113
Polymers115,6022
Non-polymers1,48811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-70 kcal/mol
Surface area39200 Å2
MethodPISA
2
C: Proline--tRNA ligase
D: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,04811
Polymers115,6022
Non-polymers1,4459
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-57 kcal/mol
Surface area38290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.020, 140.600, 187.090
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, 4 molecules ABCD

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


Mass: 57801.188 Da / Num. of mol.: 4 / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I5R7, proline-tRNA ligase

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Non-polymers , 6 types, 76 molecules

#2: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical
ChemComp-1XK / 4-[(3S)-3-cyclopropyl-3-(hydroxymethyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide


Mass: 477.531 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H28FN5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.12 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), 37.5 % v/v ...Details: 0.12 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), 37.5 % v/v Precipitant (25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.39→46.87 Å / Num. obs: 86094 / % possible obs: 99.5 % / Redundancy: 9.3 % / CC1/2: 1 / Rrim(I) all: 0.137 / Net I/σ(I): 12.7
Reflection shellResolution: 2.39→2.53 Å / Mean I/σ(I) obs: 0.72 / Num. unique obs: 13406 / CC1/2: 0.34 / Rrim(I) all: 2.547 / % possible all: 97.1

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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: 2.394→41.902 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 4269 4.99 %
Rwork0.1748 81209 -
obs0.1778 85478 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.21 Å2 / Biso mean: 74.829 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.394→41.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15772 0 197 56 16025
Biso mean--70.01 62.45 -
Num. residues----1921
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.394-2.42120.40961200.365236488
2.4212-2.44970.41931370.3365262099
2.4497-2.47950.35071430.3172707100
2.4795-2.51090.36331420.29762700100
2.5109-2.5440.35461400.28392670100
2.544-2.57880.31831420.28142690100
2.5788-2.61560.35511420.28132688100
2.6156-2.65470.31871420.26632696100
2.6547-2.69610.35221420.26552704100
2.6961-2.74030.31471410.26272674100
2.7403-2.78760.27041400.23712667100
2.7876-2.83830.29281430.23862719100
2.8383-2.89280.32781430.22292699100
2.8928-2.95190.28261430.2182722100
2.9519-3.0160.29571410.20912688100
3.016-3.08620.28411420.20552689100
3.0862-3.16330.28361430.20762718100
3.1633-3.24880.27811430.20822721100
3.2488-3.34440.26251420.19082705100
3.3444-3.45230.23331430.17192713100
3.4523-3.57560.27391430.16872721100
3.5756-3.71870.2361440.16532726100
3.7187-3.88780.23281430.15512722100
3.8878-4.09260.20281440.15422733100
4.0926-4.34880.20521450.14222747100
4.3488-4.68420.19491440.12952744100
4.6842-5.15480.1931460.13082764100
5.1548-5.89890.19251460.15382775100
5.8989-7.42530.19211480.17112815100
7.4253-41.90.15941520.1385290899
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)
11.9409-0.40780.41812.2601-0.49191.36940.0362-0.2508-0.22880.098-0.0484-0.10510.2940.0254-0.04350.4507-0.01160.00740.4420.05050.44330.973-30.9489-17.0683
20.8647-0.16440.62221.13150.2760.50450.1044-0.39510.15430.5967-0.03720.1967-0.18130.1311-0.03110.7693-0.06490.09850.66750.00490.596927.4222-5.0212-10.3804
30.9937-0.81080.06461.554-0.68051.5407-0.032-0.19-0.04920.28120.12490.2263-0.2308-0.0099-0.08970.4783-0.00550.0440.44680.04520.466121.1738-11.1608-14.5337
42.6682-0.1782-0.22992.9511-0.3292.4615-0.07240.3328-0.5799-0.1467-0.025-0.33130.5320.2835-0.00420.8010.00450.00570.5696-0.07320.758732.8223-46.8739-33.9004
50.4809-0.2886-0.19281.05621.35292.51930.07130.7522-0.7508-0.5845-0.3950.4775-0.2065-0.76190.10370.7804-0.0343-0.03370.7005-0.04280.791415.8122-40.447-28.929
62.1006-0.7202-0.85411.76270.23733.68820.0144-0.19120.01090.20620.07760.1787-0.0949-0.4174-0.08790.5333-0.0450.06140.54380.14650.54315.5459-26.32130.2073
71.0957-0.3610.09652.5787-0.75490.9963-0.0407-0.2458-0.03190.1965-0.031-0.2839-0.06370.16120.11480.3774-0.0159-0.00070.47230.04640.462643.6377-11.5766-21.2353
82.32810.3332-0.56463.115-1.40251.1127-0.0360.16170.1771-0.2263-0.2065-0.40530.16560.28040.17910.49320.04040.10330.53590.04790.506954.5275-12.6796-33.6642
91.0956-0.51180.29233.8091-1.47621.7923-0.0381-0.02280.00540.2317-0.4655-0.89260.13280.55790.22340.42720.01310.06890.61210.1110.568154.1297-23.4378-24.9657
101.86790.38561.31671.65350.32743.3463-0.1093-0.11170.3049-0.1719-0.10850.0883-0.1959-0.11460.1190.7409-0.0442-0.03160.557-0.04050.628125.75335.1045-44.0184
113.0234-0.625-0.09983.3670.99083.2061-0.0190.06360.0395-0.3874-0.14940.3508-0.1091-0.27850.10970.6516-0.0349-0.09240.51860.01530.614821.67784.4762-47.0255
123.41340.49640.00161.13570.06880.8150.02320.00070.5139-0.0255-0.1885-0.3127-0.06050.4420.15020.5715-0.07320.06160.58070.11070.667956.12791.0944-39.2893
133.51040.60811.16360.5760.11850.5176-0.121-0.1505-0.06580.1137-0.0635-1.33350.09590.72070.1290.5615-0.05170.18130.84860.12351.247172.3433-4.1319-36.0669
142.14240.0577-0.7942.47990.41391.3687-0.26360.2556-0.2086-0.56240.0358-0.11240.349-0.02240.12840.7486-0.05240.15160.45920.04010.498651.28396.64813.6286
151.1935-0.68240.98782.031-0.36130.7280.16440.45310.3707-0.79490.0829-0.0004-0.4-0.0310.01140.8522-0.0660.07120.79550.11570.679551.405632.64919.6145
160.7526-0.3618-0.4131.6263-0.04420.6643-0.22840.45110.2743-0.74490.20530.1192-0.2864-0.0231-0.06830.986-0.0714-0.01340.6350.13950.512146.019834.1236.0213
171.6023-0.1946-0.25981.5815-1.33951.504-0.09180.1903-0.0503-0.63120.0214-0.0906-0.007-0.02480.06490.54610.00530.08480.52330.04750.515755.931326.370613.321
181.28670.1511-0.39983.9551.55411.7164-0.1338-0.0125-0.1537-0.57710.0727-0.8708-0.00010.30360.02210.49310.0170.13780.50110.0530.574265.890824.205814.8612
191.92490.6450.74743.79970.95161.0193-0.24010.4396-0.0563-0.49740.37170.1630.5055-0.1674-0.11170.90920.07680.12960.56440.05170.623348.7571-9.157925.6092
202.52940.6180.39143.5518-1.37062.6522-0.1099-0.128-0.3212-0.18660.18460.11510.5602-0.269-0.16490.82690.02070.1620.54930.02690.694947.219-11.154830.2599
211.55810.4708-0.66191.38120.18882.2617-0.28610.0895-0.3724-0.5614-0.0784-0.72770.24460.25050.29850.79760.16460.29620.5649-0.03210.809670.95533.756611.9182
221.1163-0.0125-0.97450.35580.21941.2446-0.05790.4216-0.3129-0.55760.1222-1.2645-0.04610.41540.05630.9037-0.05790.5220.7527-0.09191.19379.998115.14452.9521
230.48540.804-0.38843.50990.64381.78620.09570.14260.1848-0.2514-0.04270.3836-0.0677-0.1957-0.00650.38050.0233-0.04020.5240.06450.531240.538535.778626.3159
241.19280.30370.57471.81061.27521.4332-0.02370.4603-0.1285-0.9522-0.05090.32740.14290.1185-0.07630.816-0.0538-0.1140.7135-0.01550.625134.947517.90386.1831
251.76310.4734-0.05722.43790.0911.7717-0.14450.23830.1887-0.23730.04430.51560.219-0.40820.03810.446-0.0525-0.03930.57870.07250.493530.101719.721.0115
260.92370.3648-0.34890.19540.22861.88290.4986-0.2526-0.94561.2556-0.3861-1.08030.82820.7431-0.16820.7375-0.053-0.34550.6670.1630.819260.425138.723948.249
272.96831.87750.3293.531-0.1341.0790.4133-0.36560.10980.8105-0.4014-0.1098-0.0479-0.173-0.10430.6682-0.0350.00520.5591-0.03090.563745.200639.077145.976
280.3070.3461-0.85721.5609-1.33532.29650.34710.80010.6996-1.17440.14120.69050.5264-1.2397-0.07170.5180.2654-0.10481.07850.31151.392411.136.078224.9698
290.52240.24740.30490.2320.31520.3599-0.16140.42331.2699-0.55380.32151.07480.0198-0.9570.03560.50790.0474-0.03991.27980.17921.45386.46330.042729.017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 252 through 308 )A252 - 308
2X-RAY DIFFRACTION2chain 'A' and (resid 309 through 338 )A309 - 338
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 523 )A339 - 523
4X-RAY DIFFRACTION4chain 'A' and (resid 524 through 620 )A524 - 620
5X-RAY DIFFRACTION5chain 'A' and (resid 621 through 659 )A621 - 659
6X-RAY DIFFRACTION6chain 'A' and (resid 660 through 746 )A660 - 746
7X-RAY DIFFRACTION7chain 'B' and (resid 252 through 416 )B252 - 416
8X-RAY DIFFRACTION8chain 'B' and (resid 417 through 483 )B417 - 483
9X-RAY DIFFRACTION9chain 'B' and (resid 484 through 523 )B484 - 523
10X-RAY DIFFRACTION10chain 'B' and (resid 524 through 551 )B524 - 551
11X-RAY DIFFRACTION11chain 'B' and (resid 552 through 620 )B552 - 620
12X-RAY DIFFRACTION12chain 'B' and (resid 621 through 720 )B621 - 720
13X-RAY DIFFRACTION13chain 'B' and (resid 721 through 746 )B721 - 746
14X-RAY DIFFRACTION14chain 'C' and (resid 252 through 309 )C252 - 309
15X-RAY DIFFRACTION15chain 'C' and (resid 310 through 338 )C310 - 338
16X-RAY DIFFRACTION16chain 'C' and (resid 339 through 371 )C339 - 371
17X-RAY DIFFRACTION17chain 'C' and (resid 372 through 416 )C372 - 416
18X-RAY DIFFRACTION18chain 'C' and (resid 417 through 523 )C417 - 523
19X-RAY DIFFRACTION19chain 'C' and (resid 524 through 551 )C524 - 551
20X-RAY DIFFRACTION20chain 'C' and (resid 552 through 620 )C552 - 620
21X-RAY DIFFRACTION21chain 'C' and (resid 621 through 696 )C621 - 696
22X-RAY DIFFRACTION22chain 'C' and (resid 697 through 746 )C697 - 746
23X-RAY DIFFRACTION23chain 'D' and (resid 252 through 309 )D252 - 309
24X-RAY DIFFRACTION24chain 'D' and (resid 310 through 345 )D310 - 345
25X-RAY DIFFRACTION25chain 'D' and (resid 346 through 539 )D346 - 539
26X-RAY DIFFRACTION26chain 'D' and (resid 540 through 569 )D540 - 569
27X-RAY DIFFRACTION27chain 'D' and (resid 570 through 659 )D570 - 659
28X-RAY DIFFRACTION28chain 'D' and (resid 660 through 720 )D660 - 720
29X-RAY DIFFRACTION29chain 'D' and (resid 721 through 746 )D721 - 746

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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