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- PDB-7wal: Glutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) in co... -

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Basic information

Entry
Database: PDB / ID: 7wal
TitleGlutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) in complex with Co
ComponentsGlutamyl-tRNA synthetase
KeywordsLIGASE / ERS / GluRS / GLUTAMYL-TRNA SYNTHETASE / AMINOACYL-TRNA SYNTHETAS / AMINOACYLATION / Cobalt
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
BETA-MERCAPTOETHANOL / : / glutamate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 1.1Apr 3, 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: Glutamyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,98513
Polymers61,3291
Non-polymers65612
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-81 kcal/mol
Surface area22840 Å2
Unit cell
Length a, b, c (Å)158.730, 46.110, 95.350
Angle α, β, γ (deg.)90.000, 110.730, 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 (E. coli) / References: UniProt: Q8IDK7, glutamate-tRNA ligase
#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
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: 0.984 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: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.29→46.1 Å / Num. obs: 29435 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 1 / Rrim(I) all: 0.07 / Net I/σ(I): 14.8
Reflection shellResolution: 2.29→2.35 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2036 / CC1/2: 0.69 / Rrim(I) all: 1.378 / % possible all: 95

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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: INYL

Resolution: 2.29→46.098 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 1472 5 %
Rwork0.2085 27944 -
obs0.2108 29416 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.17 Å2 / Biso mean: 77.0435 Å2 / Biso min: 46.13 Å2
Refinement stepCycle: final / Resolution: 2.29→46.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 15 24 3835
Biso mean--109.77 68.5 -
Num. residues----484
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.29-2.36270.36221270.328241196
2.3627-2.44710.3361340.29262536100
2.4471-2.54510.30711320.27752513100
2.5451-2.66090.33131330.24422535100
2.6609-2.80120.33031330.25492514100
2.8012-2.97660.31291340.24732548100
2.9766-3.20640.27181350.24242555100
3.2064-3.5290.29521330.22842543100
3.529-4.03940.25231340.20192533100
4.0394-5.08810.19091370.16182603100
5.0881-46.0980.24171400.19342653100
Refinement TLS params.Method: refined / Origin x: -27.4565 Å / Origin y: -11.369 Å / Origin z: 20.1246 Å
111213212223313233
T0.5911 Å2-0.0015 Å2-0.0334 Å2-0.6573 Å2-0.053 Å2--0.6786 Å2
L0.3325 °2-0.1021 °2-0.572 °2-1.2244 °21.7692 °2--3.8668 °2
S-0.0097 Å °-0.2387 Å °0.0427 Å °-0.0401 Å °0.1764 Å °-0.0551 Å °-0.2665 Å °0.5013 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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