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- PDB-4q15: Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA... -

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Basic information

Entry
Database: PDB / ID: 4q15
TitleCrystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Halofuginone and AMPPNP in space group P212121 at 2.35 A
ComponentsProline--tRNA ligase
KeywordsLIGASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Prolyl-tRNA 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-HFG / Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acs Infect Dis. / Year: 2017
Title: Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium falciparum Drug Target, Prolyl-tRNA-synthetase.
Authors: Hewitt, S.N. / Dranow, D.M. / Horst, B.G. / Abendroth, J.A. / Forte, B. / Hallyburton, I. / Jansen, C. / Baragana, B. / Choi, R. / Rivas, K.L. / Hulverson, M.A. / Dumais, M. / Edwards, T.E. ...Authors: Hewitt, S.N. / Dranow, D.M. / Horst, B.G. / Abendroth, J.A. / Forte, B. / Hallyburton, I. / Jansen, C. / Baragana, B. / Choi, R. / Rivas, K.L. / Hulverson, M.A. / Dumais, M. / Edwards, T.E. / Lorimer, D.D. / Fairlamb, A.H. / Gray, D.W. / Read, K.D. / Lehane, A.M. / Kirk, K. / Myler, P.J. / Wernimont, A. / Walpole, C. / Stacy, R. / Barrett, L.K. / Gilbert, I.H. / Van Voorhis, W.C.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name / _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.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)120,05011
Polymers117,9732
Non-polymers2,0779
Water4,918273
1
A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9324
Polymers58,9861
Non-polymers9453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1187
Polymers58,9861
Non-polymers1,1316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-34 kcal/mol
Surface area35640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.580, 78.090, 167.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 58986.496 Da / Num. of mol.: 2 / Fragment: UNP residues 249-746
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: proRS, PFL0670c / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I5R7, proline-tRNA ligase

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Non-polymers , 5 types, 282 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#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.: 2 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Comment: alkaloid, medication*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for ~5min, then added 1 to 1 with Wiz1/2(a10): 20% PEG-2000 MME, 0.1M Tris base/HCl, pH=7.0, cryoprotected with ...Details: Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for ~5min, then added 1 to 1 with Wiz1/2(a10): 20% PEG-2000 MME, 0.1M Tris base/HCl, pH=7.0, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 42793 / Num. obs: 42603 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.064 / Χ2: 0.963 / Net I/σ(I): 19.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.35-2.410.5473.2416238309099.9
2.41-2.480.4813.715970304199.7
2.48-2.550.3874.5515547295599.8
2.55-2.630.3245.4114975285799.8
2.63-2.710.2756.3314603279299.5
2.71-2.810.2227.7413955268899.9
2.81-2.910.1799.3613447259199.7
2.91-3.030.13212.2713114253099.9
3.03-3.170.10714.6412358239199.5
3.17-3.320.07819.2211815231199.6
3.32-3.50.05525.2711173220099.5
3.5-3.720.04530.5310485208799.6
3.72-3.970.03835.959821196599.7
3.97-4.290.03140.619086183899.7
4.29-4.70.02747.588258169499.6
4.7-5.250.02648.587592156699.5
5.25-6.070.02744.956620137899.8
6.07-7.430.02547.335516117699.7
7.43-10.510.01957.94414094299.5
10.510.01754179251188.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.4 Å45.81 Å
Translation7.4 Å45.81 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXdev_1659refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OLF

4olf


Resolution: 2.35→37.331 Å / FOM work R set: 0.8245 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 2113 4.97 %
Rwork0.195 --
obs0.1962 42514 99.54 %
all-44627 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.84 Å2 / Biso mean: 44.51 Å2 / Biso min: 21.37 Å2
Refinement stepCycle: LAST / Resolution: 2.35→37.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7190 0 124 273 7587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037514
X-RAY DIFFRACTIONf_angle_d0.75710247
X-RAY DIFFRACTIONf_chiral_restr0.0291124
X-RAY DIFFRACTIONf_plane_restr0.0041287
X-RAY DIFFRACTIONf_dihedral_angle_d14.7462644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3499-2.40460.31581390.270626402779100
2.4046-2.46470.33081340.261826792813100
2.4647-2.53130.26781460.239426582804100
2.5313-2.60580.23241560.242726512807100
2.6058-2.68990.26751440.230426312775100
2.6899-2.7860.25541480.239426512799100
2.786-2.89750.27711340.229127062840100
2.8975-3.02930.29431290.221226772806100
3.0293-3.1890.2561150.220427022817100
3.189-3.38860.21091430.20392679282299
3.3886-3.65010.20911360.18727102846100
3.6501-4.0170.18641500.17826992849100
4.017-4.59740.1691580.154327172875100
4.5974-5.78870.20851360.163527622898100
5.7887-37.33530.19031450.17882839298498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7672-0.1412-0.050.90630.10321.37030.02690.016-0.0217-0.0297-0.026-0.01380.03780.00470.00150.2733-0.0399-0.00640.2604-0.02020.2796-7.04334.1518-33.6845
20.63140.0672-0.05210.7883-0.07581.09520.0643-0.1399-0.02650.1869-0.08060.11410.077-0.06520.00960.3098-0.04580.03250.3276-0.01360.278-10.694314.5879-3.8724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 251:746)A251 - 746
2X-RAY DIFFRACTION2(chain B and resid 253:746)B253 - 746

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