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- PDB-7v9d: Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex w... -

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Basic information

Entry
Database: PDB / ID: 7v9d
TitlePlasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with inhibitor L95 and azetidine
ComponentsProline--tRNA ligase
KeywordsLIGASE / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / DOUBLE DRUG
Function / homology
Function and homology information


Ala-tRNA(Pro) hydrolase activity / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ATP binding / cytoplasm
Similarity search - Function
YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa / 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 / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa / 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
(2S)-azetidine-2-carboxylic acid / ACETATE ION / 1,4-BUTANEDIOL / Chem-JE6 / Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.937 Å
AuthorsManickam, Y. / Malhotra, N. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
CitationJournal: To Be Published
Title: Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with inhibitor L95 and azetidine
Authors: Manickam, Y. / Malhotra, N. / Sharma, A.
History
DepositionAug 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)58,6128
Polymers57,8011
Non-polymers8117
Water5,332296
1
A: Proline--tRNA ligase
hetero molecules

A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,22416
Polymers115,6022
Non-polymers1,62214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area6920 Å2
ΔGint-13 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.560, 103.560, 127.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 57801.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
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, 303 molecules

#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-02A / (2S)-azetidine-2-carboxylic acid


Type: L-peptide linking / Mass: 101.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
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 (Imidazole, MES monohydrate), 30 % 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 (Imidazole, MES monohydrate), 30 % v/v Precipitant (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 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.937→47.98 Å / Num. obs: 59069 / % possible obs: 99.7 % / Redundancy: 20.1 % / CC1/2: 1 / Rrim(I) all: 0.082 / Net I/σ(I): 24.3
Reflection shellResolution: 1.937→2.05 Å / Num. unique obs: 9279 / CC1/2: 0.9 / Rrim(I) all: 0.11 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDQ

4ydq


Resolution: 1.937→42.304 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 2007 3.4 %
Rwork0.1701 57020 -
obs0.1711 59027 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.05 Å2 / Biso mean: 44.1971 Å2 / Biso min: 25.25 Å2
Refinement stepCycle: final / Resolution: 1.937→42.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 57 300 4302
Biso mean--44.71 51.49 -
Num. residues----486
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9372-1.98570.37971370.3173385695
1.9857-2.03940.28321440.25084029100
2.0394-2.09940.21031400.20754030100
2.0994-2.16710.23831450.19624044100
2.1671-2.24460.21991440.18534052100
2.2446-2.33440.23151440.18484035100
2.3344-2.44070.23031380.1854066100
2.4407-2.56930.20611460.17764052100
2.5693-2.73030.21431410.18214092100
2.7303-2.9410.25561440.1824088100
2.941-3.23690.20321450.17584094100
3.2369-3.70510.18641430.16384112100
3.7051-4.6670.15421420.13884160100
4.667-42.3040.18661540.15944310100
Refinement TLS params.Method: refined / Origin x: 10.2843 Å / Origin y: -34.4343 Å / Origin z: -6.3642 Å
111213212223313233
T0.3544 Å20.0137 Å20.0068 Å2-0.318 Å2-0.0086 Å2--0.3306 Å2
L0.9284 °20.1441 °20.1171 °2-0.706 °20.0926 °2--1.0531 °2
S-0.005 Å °-0.0581 Å °-0.0395 Å °0.0991 Å °-0.0528 Å °0.06 Å °-0.0746 Å °-0.1736 Å °0 Å °
Refinement TLS groupSelection details: all

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