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- PDB-4twa: Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium... -

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Basic information

Entry
Database: PDB / ID: 4twa
TitleCrystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum
ComponentsProline--tRNA ligase
KeywordsLIGASE / Protein translation / Halofuginone / Malaria / Inhibitor / PRS / Synthetase
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
C-terminal domain of ProRS / 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 ...C-terminal domain of ProRS / 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 / Translation Initiation Factor IF3 / Anticodon-binding domain / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJain, V. / Yogavel, M. / Sharma, A.
CitationJournal: J. Struct. Funct. Genomics / Year: 2014
Title: Structural and functional analysis of the anti-malarial drug target prolyl-tRNA synthetase.
Authors: Jain, V. / Kikuchi, H. / Oshima, Y. / Sharma, A. / Yogavel, M.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proline--tRNA ligase
B: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,87219
Polymers115,6022
Non-polymers1,26917
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-203 kcal/mol
Surface area40040 Å2
MethodPISA
2
A: Proline--tRNA ligase
B: Proline--tRNA ligase
hetero molecules

A: Proline--tRNA ligase
B: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,74438
Polymers231,2054
Non-polymers2,53934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area16340 Å2
ΔGint-427 kcal/mol
Surface area77560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.240, 104.106, 111.420
Angle α, β, γ (deg.)90.00, 92.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Proline--tRNA ligase / Prolyl-tRNA synthetase / ProRS


Mass: 57801.188 Da / Num. of mol.: 2 / Fragment: UNP residues 254-746
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: proRS, PFL0670c / Plasmid: pETM41 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q8I5R7, proline-tRNA ligase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.8 M lithium sulphate monohydrate and 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 30738 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 12.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K86

4k86


Resolution: 3→38.79 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 1583 5.18 %Random selection
Rwork0.172 ---
obs0.1753 30581 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→38.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7786 0 61 57 7904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098121
X-RAY DIFFRACTIONf_angle_d1.22711028
X-RAY DIFFRACTIONf_dihedral_angle_d16.0632980
X-RAY DIFFRACTIONf_chiral_restr0.0471181
X-RAY DIFFRACTIONf_plane_restr0.0061387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0005-3.09720.34631380.23482629X-RAY DIFFRACTION95
3.0972-3.20780.34241320.22482628X-RAY DIFFRACTION95
3.2078-3.3360.30591440.20322621X-RAY DIFFRACTION95
3.336-3.48760.29921390.18322613X-RAY DIFFRACTION95
3.4876-3.67120.29751530.19622614X-RAY DIFFRACTION94
3.6712-3.90070.27051620.15822599X-RAY DIFFRACTION94
3.9007-4.2010.20151440.15412640X-RAY DIFFRACTION95
4.201-4.62230.19891280.13222643X-RAY DIFFRACTION95
4.6223-5.28770.20831320.14462667X-RAY DIFFRACTION95
5.2877-6.64880.23241280.17112648X-RAY DIFFRACTION95
6.6488-29.08660.20721430.17262707X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 35.2759 Å / Origin y: 22.1673 Å / Origin z: 32.9794 Å
111213212223313233
T0.1159 Å2-0.036 Å2-0.0092 Å2-0.1182 Å20.0034 Å2--0.0872 Å2
L0.1165 °2-0.058 °2-0.0171 °2-0.3603 °20.1325 °2--0.287 °2
S-0.0555 Å °0.0001 Å °-0.0405 Å °-0.1367 Å °0.005 Å °-0.0027 Å °-0.0674 Å °0.0012 Å °-0.0105 Å °
Refinement TLS groupSelection details: all

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