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- PDB-7by6: Plasmodium vivax cytoplasmic Phenylalanyl-tRNA synthetase in comp... -

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Basic information

Entry
Database: PDB / ID: 7by6
TitlePlasmodium vivax cytoplasmic Phenylalanyl-tRNA synthetase in complex with BRD1389
Components(Phenylalanyl-tRNA synthetase beta chain, putative) x 2
KeywordsLIGASE / AMINOACYLATION / AMINOACYL-TRNA SYNTHETASE / TRNA-BINDING / ATP-BINDING / AUXILIARY POCKET / HETEROTETRAMERIC
Function / homology
Function and homology information


phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / RNA binding / ATP 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 / 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.
Similarity search - Domain/homology
Chem-FB9 / Phenylalanyl-tRNA synthetase beta subunit / Phenylalanine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.997 Å
AuthorsMalhotra, N. / Manmohan, S. / Harlos, K. / Melillo, B. / Schreiber, S.L. / Manickam, Y. / Sharma, S.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of malaria parasite phenylalanine tRNA-synthetase inhibition by bicyclic azetidines.
Authors: Sharma, M. / Malhotra, N. / Yogavel, M. / Harlos, K. / Melillo, B. / Comer, E. / Gonse, A. / Parvez, S. / Mitasev, B. / Fang, F.G. / Schreiber, S.L. / Sharma, A.
History
DepositionApr 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylalanyl-tRNA synthetase beta chain, putative
B: Phenylalanyl-tRNA synthetase beta chain, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4484
Polymers106,8562
Non-polymers5922
Water00
1
A: Phenylalanyl-tRNA synthetase beta chain, putative
B: Phenylalanyl-tRNA synthetase beta chain, putative
hetero molecules

A: Phenylalanyl-tRNA synthetase beta chain, putative
B: Phenylalanyl-tRNA synthetase beta chain, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,8958
Polymers213,7114
Non-polymers1,1844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area20840 Å2
ΔGint-124 kcal/mol
Surface area75420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.523, 74.071, 121.682
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phenylalanyl-tRNA synthetase beta chain, putative


Mass: 35323.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_081300 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: A5K9S0, phenylalanine-tRNA ligase
#2: Protein Phenylalanyl-tRNA synthetase beta chain, putative


Mass: 71532.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_090880 / Plasmid: pETM41 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: A5K464, phenylalanine-tRNA ligase
#3: Chemical ChemComp-FB9 / (3S,4R,8R,9R,10S)-N-(4-cyclopropyloxyphenyl)-10-(methoxymethyl)-3,4-bis(oxidanyl)-9-[4-(2-phenylethynyl)phenyl]-1,6-diazabicyclo[6.2.0]decane-6-carboxamide


Mass: 567.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H37N3O5 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 3% w/v poly-gama-glutamic acid (Na+ form, low molecular weight), 3% w/v PEG20000, 0.1 M ammonium sulphate, 0.3 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 2.997→136.5 Å / Num. obs: 25453 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.921 / Rrim(I) all: 0.145 / Net I/σ(I): 8.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1186 / CC1/2: 0.741 / Rrim(I) all: 1.288 / % possible all: 94.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L4G

3l4g


Resolution: 2.997→121.7824 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2882 1296 5.11 %
Rwork0.2137 24079 -
obs0.2176 25375 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.44 Å2 / Biso mean: 91.2782 Å2 / Biso min: 47.14 Å2
Refinement stepCycle: final / Resolution: 2.997→121.7824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6873 0 43 0 6916
Biso mean--63.42 --
Num. residues----905
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.997-3.11650.38931300.2935257497
3.1165-3.25840.3951480.27522628100
3.2584-3.43020.32141550.23932618100
3.4302-3.64510.371380.21472650100
3.6451-3.92660.29431430.20912677100
3.9266-4.32170.23931540.18722651100
4.3217-4.94710.24151440.16762698100
4.9471-6.23280.30321470.23262724100
6.2328-121.78240.26741370.2175285999
Refinement TLS params.Method: refined / Origin x: 21.8053 Å / Origin y: 3.5471 Å / Origin z: 25.3067 Å
111213212223313233
T0.7068 Å2-0.0801 Å2-0.072 Å2-0.6935 Å20.0964 Å2--0.6182 Å2
L1.8371 °21.3907 °20.5193 °2-1.434 °20.6892 °2--0.5375 °2
S0.2636 Å °-0.3099 Å °-0.317 Å °0.24 Å °-0.189 Å °-0.2679 Å °0.0629 Å °0.1267 Å °0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA271 - 601
2X-RAY DIFFRACTION1allB0 - 701

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