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- PDB-7dpi: Plasmodium falciparum cytoplasmic Phenylalanyl-tRNA synthetase in... -

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Basic information

Entry
Database: PDB / ID: 7dpi
TitlePlasmodium falciparum cytoplasmic Phenylalanyl-tRNA synthetase in complex with BRD7929
Components
  • Phenylalanine--tRNA ligase
  • Phenylalanyl-tRNA synthetase beta subunit
KeywordsLIGASE / AMINOACYLATION / AMINOACYL-TRNA SYNTHETASE / TRNA-BINDING / ATP-BINDING / AUXILIARY POCKET / HETEROTETRAMERIC
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / RNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Phenylalanine--tRNA ligase beta subunit, B1 domain / Phe-tRNA synthetase beta subunit B1 domain / Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / B3/B4 tRNA-binding domain ...Phenylalanine--tRNA ligase beta subunit, B1 domain / Phe-tRNA synthetase beta subunit B1 domain / Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/4 domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Putative DNA-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-B79 / phenylalanine--tRNA ligase / phenylalanine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.597 Å
AuthorsManmohan, S. / Malhotra, N. / Harlos, K. / Manickam, Y. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
CitationJournal: Structure / Year: 2022
Title: Inhibition of Plasmodium falciparum phenylalanine tRNA synthetase provides opportunity for antimalarial drug development.
Authors: Sharma, M. / Mutharasappan, N. / Manickam, Y. / Harlos, K. / Melillo, B. / Comer, E. / Tabassum, H. / Parvez, S. / Schreiber, S.L. / Sharma, A.
History
DepositionDec 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylalanine--tRNA ligase
C: Phenylalanine--tRNA ligase
B: Phenylalanyl-tRNA synthetase beta subunit
D: Phenylalanyl-tRNA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,1817
Polymers218,1114
Non-polymers1,0703
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14200 Å2
ΔGint-89 kcal/mol
Surface area89520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.648, 108.034, 140.532
Angle α, β, γ (deg.)90.000, 105.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 278 through 295 or (resid 297...
21(chain C and (resid 278 through 279 or (resid 280...
12(chain B and ((resid 4 through 8 and (name N...
22(chain D and ((resid 4 through 8 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and (resid 278 through 295 or (resid 297...
211(chain C and (resid 278 through 279 or (resid 280...
112(chain B and ((resid 4 through 8 and (name N...
212(chain D and ((resid 4 through 8 and (name N...

NCS ensembles :
ID
1
2

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Components

#1: Protein Phenylalanine--tRNA ligase


Mass: 36464.844 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I246, phenylalanine-tRNA ligase
#2: Protein Phenylalanyl-tRNA synthetase beta subunit


Mass: 72590.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pETM20 / Production host: Escherichia coli (E. coli) / References: UniProt: W7JTS1, phenylalanine-tRNA ligase
#3: Chemical ChemComp-B79 / (8R,9S,10S)-10-[(dimethylamino)methyl]-N-(4-methoxyphenyl)-9-[4-(2-phenylethynyl)phenyl]-1,6-diazabicyclo[6.2.0]decane-6-carboxamide


Mass: 522.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H38N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium malonate, 12% w/v PEG 3350, 5% v/v Ethyl acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.18
ReflectionResolution: 3.597→66.142 Å / Num. obs: 29013 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 75.926 Å2 / Rpim(I) all: 0.146 / Rrim(I) all: 0.387 / Net I/σ(I): 3.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
3.6-3.666.90.8950413831.0232.6995.8
9.76-66.156.66.8991414950.0350.09198.5

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.15RC1_3423refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.597→66.142 Å / Cross valid method: THROUGHOUT / σ(F): 2.75 / Phase error: 41.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3302 2082 7.19 %
Rwork0.2936 26932 -
obs0.2988 28944 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.38 Å2 / Biso mean: 87.5581 Å2 / Biso min: 45.71 Å2
Refinement stepCycle: final / Resolution: 3.597→66.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11765 0 79 0 11844
Biso mean--68.99 --
Num. residues----1650
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1798X-RAY DIFFRACTION20.779TORSIONAL
12C1798X-RAY DIFFRACTION20.779TORSIONAL
21B3000X-RAY DIFFRACTION20.779TORSIONAL
22D3000X-RAY DIFFRACTION20.779TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5988-3.68880.37131410.3116187991
3.6888-3.78850.34251430.3017191192
3.7885-3.90.33521360.3126193093
3.9-4.02580.34041480.2957191092
4.0258-4.16970.30251440.3036192492
4.1697-4.33660.39771420.2881189391
4.3366-4.53390.32511480.2843190992
4.5339-4.77290.30221310.2827194494
4.7729-5.07180.33771480.2816192193
5.0718-5.46320.34151500.3074193293
5.4632-6.01270.40821430.3228193792
6.0127-6.88180.3491360.335190191
6.8818-8.6670.30731470.2926197293
8.667-64.13760.2871450.2742196992
Refinement TLS params.Method: refined / Origin x: -20.5009 Å / Origin y: -25.3999 Å / Origin z: -27.07 Å
111213212223313233
T0.5968 Å20.0269 Å2-0.165 Å2-0.5878 Å2-0.0098 Å2--0.544 Å2
L0.1072 °2-0.0928 °2-0.0279 °2-0.5531 °20.0789 °2--0.4906 °2
S-0.0302 Å °-0.1067 Å °0.0013 Å °-0.0599 Å °-0.0691 Å °-0.0148 Å °0.0163 Å °0.0141 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA277 - 701
2X-RAY DIFFRACTION1allC278 - 701
3X-RAY DIFFRACTION1allB4 - 701
4X-RAY DIFFRACTION1allD2 - 618

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