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- PDB-7wai: Glutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) -

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Basic information

Entry
Database: PDB / ID: 7wai
TitleGlutamyl-tRNA synthetase from Plasmodium falciparum (PfERS)
ComponentsGlutamyl-tRNA synthetase
KeywordsLIGASE / ERS / GluRS / GLUTAMYL-TRNA SYNTHETASE / AMINOACYL-TRNA SYNTHETAS / AMINOACYLATION
Function / homology
Function and homology information


methionyl glutamyl tRNA synthetase complex / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / ATP binding / metal ion binding / cytosol
Similarity search - Function
Glutamine-tRNA ligase, alpha-bundle domain superfamily / : / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain ...Glutamine-tRNA ligase, alpha-bundle domain superfamily / : / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily
Similarity search - Domain/homology
glutamate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsSharma, V. / Manickam, Y. / Harlos, K. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
CitationJournal: Mol.Biochem.Parasitol. / Year: 2022
Title: Structural characterization of glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum.
Authors: Sharma, V.K. / Chhibber-Goel, J. / Yogavel, M. / Sharma, A.
History
DepositionDec 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Glutamyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5076
Polymers61,3291
Non-polymers1775
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-39 kcal/mol
Surface area23780 Å2
Unit cell
Length a, b, c (Å)157.460, 47.363, 94.449
Angle α, β, γ (deg.)90.000, 109.100, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutamyl-tRNA synthetase


Mass: 61329.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1349200 / Plasmid: pETM41 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IDK7, glutamate-tRNA ligase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.105→74.4 Å / Num. obs: 35766 / % possible obs: 92.6 % / Redundancy: 6.3 % / CC1/2: 1 / Rrim(I) all: 0.059 / Net I/σ(I): 15
Reflection shellResolution: 2.105→2.142 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1100 / CC1/2: 0.42 / Rrim(I) all: 2.02

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NYL

1nyl


Resolution: 2.105→45.373 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 1731 4.84 %
Rwork0.1944 34001 -
obs0.1966 35732 92.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.76 Å2 / Biso mean: 68.9563 Å2 / Biso min: 38.85 Å2
Refinement stepCycle: final / Resolution: 2.105→45.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 5 90 4210
Biso mean--85.31 59.42 -
Num. residues----506
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1052-2.16720.3672830.3347183060
2.1672-2.23710.33511190.3078211671
2.2371-2.31710.31160.2773256384
2.3171-2.40980.30191570.2465291796
2.4098-2.51950.28651590.24573037100
2.5195-2.65230.2911680.23983039100
2.6523-2.81850.25681560.24993041100
2.8185-3.0360.28041540.24643047100
3.036-3.34150.28041470.22823064100
3.3415-3.82480.24861660.19633056100
3.8248-4.8180.20751560.1473100100
4.818-45.3730.2051500.16413191100
Refinement TLS params.Method: refined / Origin x: -26.3118 Å / Origin y: -9.4903 Å / Origin z: 19.9167 Å
111213212223313233
T0.5112 Å20.0158 Å2-0.0124 Å2-0.5143 Å2-0.0257 Å2--0.551 Å2
L0.491 °20.2157 °20.0171 °2-1.0369 °21.2145 °2--2.3112 °2
S0.0326 Å °-0.1525 Å °0.0479 Å °-0.0249 Å °0.1118 Å °-0.0758 Å °-0.1668 Å °0.2312 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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