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- PDB-5xip: Crystal Structure of Eimeria tenella Prolyl-tRNA Synthetase (EtPR... -

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Basic information

Entry
Database: PDB / ID: 5xip
TitleCrystal Structure of Eimeria tenella Prolyl-tRNA Synthetase (EtPRS) in complex with Halofuginone
ComponentsProlyl-tRNA synthetase, putative
KeywordsLIGASE / Protein Translation / PRS / Synthetase / Inhibitor / Infectious Disease
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / cytoplasm
Similarity search - Function
C-terminal domain of ProRS / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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 / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-HFG / proline--tRNA ligase
Similarity search - Component
Biological speciesEimeria tenella (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsJain, V. / Manickam, Y. / Sharma, A.
CitationJournal: Structure / Year: 2017
Title: Targeting Prolyl-tRNA Synthetase to Accelerate Drug Discovery against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis
Authors: Jain, V. / Yogavel, M. / Kikuchi, H. / Oshima, Y. / Hariguchi, N. / Matsumoto, M. / Goel, P. / Touquet, B. / Jumani, R.S. / Tacchini-Cottier, F. / Harlos, K. / Huston, C.D. / Hakimi, M.A. / Sharma, A.
History
DepositionApr 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl-tRNA synthetase, putative
B: Prolyl-tRNA synthetase, putative
C: Prolyl-tRNA synthetase, putative
D: Prolyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,78216
Polymers229,0014
Non-polymers3,78112
Water28816
1
A: Prolyl-tRNA synthetase, putative
B: Prolyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3918
Polymers114,5012
Non-polymers1,8906
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-45 kcal/mol
Surface area37350 Å2
MethodPISA
2
C: Prolyl-tRNA synthetase, putative
D: Prolyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3918
Polymers114,5012
Non-polymers1,8906
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-42 kcal/mol
Surface area36780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.757, 138.757, 425.671
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Prolyl-tRNA synthetase, putative


Mass: 57250.336 Da / Num. of mol.: 4 / Fragment: UNP residues 253-747
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eimeria tenella (eukaryote) / Gene: ETH_00000045 / Plasmid: PETM41 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: U6KWI1
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-HFG / 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one / Halofuginone


Mass: 414.681 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.44 Å3/Da / Density % sol: 64.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10%(w/v) PEG 4K, 20%(v/v) glycerol, 0.03M of each divalent cation and 0.1M MES/imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.588
11K, H, -L20.412
ReflectionResolution: 3.1→50 Å / Num. obs: 53383 / % possible obs: 95.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.099 / Χ2: 1.24 / Net I/σ(I): 7.8 / Num. measured all: 213662
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.509 / Num. unique obs: 2726 / Χ2: 0.726 / % possible all: 97.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MxCuBEdata collection
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
MxCuBEdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TWA

4twa


Resolution: 3.1→41.77 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2138 / WRfactor Rwork: 0.173 / FOM work R set: 0.8025 / SU B: 17.113 / SU ML: 0.308 / SU Rfree: 0.0845 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 2003 3.8 %RANDOM
Rwork0.1801 ---
obs0.182 51005 95.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.74 Å2 / Biso mean: 58.803 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1--13 Å2-0 Å2-0 Å2
2---13 Å2-0 Å2
3---25.99 Å2
Refinement stepCycle: final / Resolution: 3.1→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14786 0 224 16 15026
Biso mean--37.3 28.21 -
Num. residues----1866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915332
X-RAY DIFFRACTIONr_angle_refined_deg1.611.95820870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01351856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9123.18676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.631152506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.30515117
X-RAY DIFFRACTIONr_chiral_restr0.1020.22279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111614
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 152 -
Rwork0.28 3727 -
all-3879 -
obs--94.91 %

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