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- PDB-5jld: Crystal Structure of Arginyl-tRNA Synthetase from Plasmodium falc... -

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Basic information

Entry
Database: PDB / ID: 5jld
TitleCrystal Structure of Arginyl-tRNA Synthetase from Plasmodium falciparum (PfRRS)
ComponentsArginyl-tRNA synthetase, putative
KeywordsLIGASE / Arginyl-tRNA Synthetase / Translation / Malaria
Function / homology
Function and homology information


arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Arginine-tRNA ligase / Arginyl tRNA synthetase N-terminal domain / Arginyl-tRNA synthetase, catalytic core domain / Arginyl tRNA synthetase N-terminal domain superfamily / tRNA synthetases class I (R) / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / DALR anticodon binding / DALR anticodon binding domain ...Arginine-tRNA ligase / Arginyl tRNA synthetase N-terminal domain / Arginyl-tRNA synthetase, catalytic core domain / Arginyl tRNA synthetase N-terminal domain superfamily / tRNA synthetases class I (R) / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / DALR anticodon binding / DALR anticodon binding domain / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Arginyl-tRNA synthetase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJain, V. / Manickam, Y. / Sharma, A.
CitationJournal: Structure / Year: 2016
Title: Dimerization of Arginyl-tRNA Synthetase by Free Heme Drives Its Inactivation in Plasmodium falciparum
Authors: Jain, V. / Yogavel, M. / Sharma, A.
History
DepositionApr 27, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginyl-tRNA synthetase, putative


Theoretical massNumber of molelcules
Total (without water)69,5151
Polymers69,5151
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25960 Å2
Unit cell
Length a, b, c (Å)46.196, 62.079, 114.640
Angle α, β, γ (deg.)90.000, 96.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arginyl-tRNA synthetase, putative


Mass: 69515.461 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: PFL0900c / Plasmid: pETM-41 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8I5M2, arginine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.69 % / Mosaicity: 0.712 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10.0%(W/V) PEG6000, 2.0%(W/V) PEG3350, 5%(V/V) MPD, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97903 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 32304 / % possible obs: 98.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.059 / Net I/av σ(I): 23.958 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.244.70.557197.8
2.24-2.284.70.449198
2.28-2.324.70.414198.2
2.32-2.374.70.352198.1
2.37-2.424.70.309198.4
2.42-2.484.70.263198.3
2.48-2.544.70.218198.5
2.54-2.614.70.185198.5
2.61-2.694.70.171198.5
2.69-2.774.70.142198.7
2.77-2.874.70.113198.9
2.87-2.994.70.098198.6
2.99-3.124.70.084198.8
3.12-3.294.70.071198.9
3.29-3.494.70.066198.9
3.49-3.764.60.055198.8
3.76-4.144.50.048198.1
4.14-4.744.50.041197
4.74-5.974.50.039198.8
5.97-504.40.034197.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q2Y

4q2y


Resolution: 2.2→41.987 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.09
RfactorNum. reflection% reflection
Rfree0.2448 1633 5.06 %
Rwork0.1843 --
obs0.1874 32264 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.02 Å2 / Biso mean: 61.2088 Å2 / Biso min: 29.62 Å2
Refinement stepCycle: final / Resolution: 2.2→41.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4407 0 0 153 4560
Biso mean---52.56 -
Num. residues----559
LS refinement shellResolution: 2.2001→2.2648 Å
Refinement TLS params.Method: refined / Origin x: -0.6045 Å / Origin y: 1.6331 Å / Origin z: 25.2755 Å
111213212223313233
T0.4176 Å20.079 Å20.0156 Å2-0.4241 Å2-0.0264 Å2--0.3559 Å2
L0.8575 °2-0.4439 °20.0314 °2-1.6636 °20.0118 °2--0.5723 °2
S-0.1488 Å °-0.1734 Å °0.1248 Å °0.3308 Å °0.1523 Å °-0.0676 Å °0.0349 Å °0.0267 Å °-0.0043 Å °
Refinement TLS groupSelection details: all

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