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- PDB-7qc2: Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ... -

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Basic information

Entry
Database: PDB / ID: 7qc2
TitleCrystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT334 and L-Proline
ComponentsProline--tRNA ligase
KeywordsLIGASE / Proline / Aminoacyl-tRNA synthetase / Protein biosynthesis
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
Chem-AJT / PROLINE / Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsJohansson, C. / Tye, M. / Payne, N.C. / Mazitschek, R. / Oppermann, U.C.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT334 and L-Proline
Authors: Johansson, C. / Tye, M. / Payne, N.C. / Mazitschek, R. / Oppermann, U.C.T.
History
DepositionNov 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3066
Polymers58,5271
Non-polymers7795
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint8 kcal/mol
Surface area21710 Å2
Unit cell
Length a, b, c (Å)103.500, 103.500, 127.510
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: 58526.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: proRS, PFL0670c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8I5R7, proline-tRNA ligase
#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-AJT / ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-[[4-[[(2~{S})-pyrrolidin-2-yl]carbonylamino]piperidin-1-yl]carbonylamino]pyrazine-2-carboxamide


Mass: 477.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H31N7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M L-Pro, 10 % PEG3350, 0.1 M Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.28→51.95 Å / Num. obs: 36445 / % possible obs: 99.6 % / Redundancy: 10.2 % / Biso Wilson estimate: 62.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.02 / Rrim(I) all: 0.065 / Net I/σ(I): 18.4 / Num. measured all: 372214 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.28-2.3410.21.6522712826620.7070.5441.7411.399.2
10.2-51.958.70.02641494760.9990.0090.02857.999.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.07 Å51.95 Å
Translation5.07 Å51.95 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.0phasing
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T7K

6t7k


Resolution: 2.28→51.95 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 1740 4.78 %
Rwork0.2277 34656 -
obs0.2289 36396 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.57 Å2 / Biso mean: 84.5212 Å2 / Biso min: 38.48 Å2
Refinement stepCycle: final / Resolution: 2.28→51.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3848 0 55 45 3948
Biso mean--66.26 70.15 -
Num. residues----492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.28-2.350.37561490.33072846299599
2.35-2.420.35441200.31822856297699
2.42-2.510.33531200.31442851297199
2.51-2.610.32811640.29142835299999
2.61-2.730.36631420.33152870301299
2.73-2.870.35221440.28122853299799
2.87-3.050.34081490.28572859300899
3.05-3.290.28671410.266628733014100
3.29-3.620.26721240.247529143038100
3.62-4.140.26211530.208129283081100
4.14-5.220.1661550.178929263081100
5.22-51.950.23821790.198730453224100
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)
13.5198-0.6064-0.1372.6223-0.90024.39090.01190.1804-0.1495-0.2829-0.14220.01710.0390.43810.11830.4917-0.0435-0.02620.4133-0.0270.3181-16.2295-40.3863-6.5205
21.6135-0.57440.15921.6451-0.15673.8768-0.01950.21010.1453-0.4144-0.1436-0.0032-0.65050.5650.2230.6275-0.0921-0.03420.4040.04370.4096-19.0709-31.5257-15.3706
31.38420.0281-1.13136.43050.23931.11590.2030.04350.02990.6407-0.4726-0.86370.08880.2170.28740.8202-0.3737-0.15491.59460.20060.953116.2727-27.27770.1295
44.79060.94031.50933.22981.0363.79730.44961.1667-0.1878-0.7776-0.3842-0.2522-0.07621.114-0.13550.78740.08050.10651.03530.08960.4768-7.8954-40.1681-32.0558
55.16461.0421-3.17761.99997.12787.4633-2.72744.4470.556-2.1920.41036.3077-2.71571.08312.35370.585-0.033-0.16290.57960.01320.6539-23.3817-35.2439-15.6641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 250 through 353 )A250 - 353
2X-RAY DIFFRACTION2chain 'A' and (resid 354 through 551 )A354 - 551
3X-RAY DIFFRACTION3chain 'A' and (resid 552 through 628 )A552 - 628
4X-RAY DIFFRACTION4chain 'A' and (resid 629 through 746 )A629 - 746

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