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- PDB-7waj: Glutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) compl... -

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Basic information

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


methionyl glutamyl tRNA synthetase complex / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / ATP binding / cytosol
Similarity search - Function
Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, 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 ...Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, 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
ADENOSINE-5'-TRIPHOSPHATE / BETA-MERCAPTOETHANOL / : / glutamate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.254 Å
AuthorsSharma, V. / Manickam, Y. / Babbar, P. / 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)62,52815
Polymers61,3291
Non-polymers1,19914
Water52229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-71 kcal/mol
Surface area23010 Å2
Unit cell
Length a, b, c (Å)158.190, 46.340, 95.320
Angle α, β, γ (deg.)90.000, 110.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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(DE3) (bacteria) / References: UniProt: Q8IDK7, glutamate-tRNA ligase

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Non-polymers , 5 types, 43 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.25→49.04 Å / Num. obs: 30851 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 1 / Rrim(I) all: 0.061 / Net I/σ(I): 16.6
Reflection shellResolution: 2.25→2.31 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2181 / CC1/2: 0.74 / Rrim(I) all: 1.468 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WAI

7wai


Resolution: 2.254→49.04 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1543 5 %
Rwork0.1989 29294 -
obs0.2012 30837 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.45 Å2 / Biso mean: 74.0568 Å2 / Biso min: 45.7 Å2
Refinement stepCycle: final / Resolution: 2.254→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 47 30 3979
Biso mean--93.83 64.94 -
Num. residues----492
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2543-2.32710.38271350.3131256497
2.3271-2.41030.33591390.28342631100
2.4103-2.50680.3521400.28512670100
2.5068-2.62090.34851380.27292621100
2.6209-2.7590.27241400.23352662100
2.759-2.93190.27161410.22622670100
2.9319-3.15820.27531390.22252639100
3.1582-3.47590.30581410.21262678100
3.4759-3.97870.24871410.19092680100
3.9787-5.0120.19581420.15482701100
5.012-49.040.21141470.18852778100
Refinement TLS params.Method: refined / Origin x: -27.3565 Å / Origin y: -9.589 Å / Origin z: 20.0558 Å
111213212223313233
T0.5829 Å2-0.0074 Å2-0.0194 Å2-0.6505 Å2-0.0682 Å2--0.6689 Å2
L0.1964 °2-0.064 °2-0.2163 °2-0.9916 °21.2928 °2--2.8225 °2
S-0.0237 Å °-0.1941 Å °0.0428 Å °0.015 Å °0.1616 Å °-0.0634 Å °-0.14 Å °0.3756 Å °0 Å °
Refinement TLS groupSelection details: all

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