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- PDB-5ifu: Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA... -

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Basic information

Entry
Database: PDB / ID: 5ifu
TitleCrystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Glyburide
ComponentsProline--tRNA ligase
KeywordsLIGASE / Plasmodium falciparum / Prolyl-tRNA synthetase / ProRS / Proline--tRNA ligase / Glyburide / Structural Genomics / Structural Genomics Consortium / SGC
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
FORMIC ACID / Chem-GBM / Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsDranow, D.M. / Hewitt, S.N. / Abendroth, J. / Structural Genomics Consortium (SGC)
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
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)119,76521
Polymers117,9732
Non-polymers1,79219
Water4,378243
1
A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,03814
Polymers58,9861
Non-polymers1,05213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7277
Polymers58,9861
Non-polymers7406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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)239,53042
Polymers235,9464
Non-polymers3,58438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area16770 Å2
ΔGint-73 kcal/mol
Surface area69910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.310, 138.310, 156.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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 (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: proRS, PFL0670c / Plasmid: PlfaA.18681.a.B4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I5R7, proline-tRNA ligase

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-GBM / 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / Glibenclamide / Glyburide / Glibenclamide


Mass: 494.004 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H28ClN3O5S / Comment: medication*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.18 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: at 22mg/ml, incubated with 5mM glyburide, then 1:1 with Morpheus(g2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each sodium formate, ammonium acetate, trisodium ...Details: at 22mg/ml, incubated with 5mM glyburide, then 1:1 with Morpheus(g2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium tartrate, sodium oxamate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.45→43.737 Å / Num. obs: 56139 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.69
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.45-2.517.50.5334.151100
2.51-2.580.4275.07199.9
2.58-2.660.3545.98199.9
2.66-2.740.2727.54199.9
2.74-2.830.2238.97199.9
2.83-2.930.18810.4199.9
2.93-3.040.14113.36199.8
3.04-3.160.10916.36199.8
3.16-3.30.09219.3199.7
3.3-3.460.07223.49199.6
3.46-3.650.06425.99199.5
3.65-3.870.05629.1199.6
3.87-4.140.05330.98199.2
4.14-4.470.04633.56199.2
4.47-4.90.04235.33199
4.9-5.480.04335.19199
5.48-6.330.0434.63198.5
6.33-7.750.03735.98198.4
7.75-10.960.0338.49197.6
10.96-43.7370.02638190.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.4 Å46.1 Å
Translation6.4 Å46.1 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXdev_1819refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q15

4q15


Resolution: 2.45→43.737 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.23
RfactorNum. reflection% reflection
Rfree0.2129 2752 4.91 %
Rwork0.185 56100 -
obs0.1863 56100 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.86 Å2 / Biso mean: 61.3991 Å2 / Biso min: 22.26 Å2
Refinement stepCycle: final / Resolution: 2.45→43.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6942 0 104 243 7289
Biso mean--76.75 52.26 -
Num. residues----883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037233
X-RAY DIFFRACTIONf_angle_d0.6689800
X-RAY DIFFRACTIONf_chiral_restr0.0261065
X-RAY DIFFRACTIONf_plane_restr0.0031243
X-RAY DIFFRACTIONf_dihedral_angle_d12.3422582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.49220.26881430.229126152758100
2.4922-2.53750.25881330.218326492782100
2.5375-2.58630.27081250.215526472772100
2.5863-2.63910.25991360.216726422778100
2.6391-2.69650.28081200.21126482768100
2.6965-2.75920.2591380.210126472785100
2.7592-2.82820.25851380.210926442782100
2.8282-2.90460.26621480.218326382786100
2.9046-2.99010.22241440.216126242768100
2.9901-3.08660.23731690.203726242793100
3.0866-3.19680.23261240.207826712795100
3.1968-3.32480.23971280.206326732801100
3.3248-3.47610.22111300.190426652795100
3.4761-3.65920.20831490.187726522801100
3.6592-3.88840.20561270.179426792806100
3.8884-4.18840.19331430.1652680282399
4.1884-4.60950.17651340.14452690282499
4.6095-5.27550.17511480.14942694284299
5.2755-6.64280.1831330.18512733286699
6.6428-43.74440.2061420.18642833297597
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)
14.2221-0.59891.34152.4598-1.01463.05010.2697-0.11120.8521-0.0177-0.13870.1817-0.09-0.364-0.13070.3067-0.08040.13830.289-0.00660.4801-40.0964-2.896828.2873
23.5711.3044-0.38393.06361.57933.01340.05180.0272-0.04930.2687-0.1130.25840.24280.18590.0330.3237-0.05550.01160.27450.01360.2707-13.7449-5.224933.881
34.35670.69670.83320.76760.1892.56780.12190.2038-0.09520.0677-0.0589-0.08040.19310.2763-0.07120.3640.00070.03370.242-0.01880.3164-18.2263-7.820521.1302
46.0941.6178-2.4882.7811-2.01245.49430.4044-0.1828-0.12640.3816-0.12750.4097-0.622-0.1907-0.23860.3695-0.05980.10730.2664-0.0430.4371-54.5973-14.968429.8886
53.27851.5292-2.44771.4918-1.55192.45970.0318-0.02410.03230.0516-0.01110.20880.0896-0.26880.01230.3342-0.0810.03090.3562-0.03910.4179-53.0558-19.798527.3746
63.1511-0.83851.23173.1548-1.343.0122-0.01070.16620.3514-0.1231-0.0626-0.0564-0.24940.11920.08050.26380.01940.01930.21510.03450.2794-23.8529-1.22180.4216
73.9984-0.44891.28365.2217-1.08616.07520.097-0.3284-0.07820.3851-0.0522-0.47920.40380.3836-0.06050.4687-0.10180.0240.40140.01040.3618-5.0429-4.754253.6428
87.7419-1.35352.37161.7215-0.83582.47260.1379-0.62970.3260.2069-0.26450.30830.2577-0.77530.1050.5048-0.20710.1460.6067-0.16840.3814-36.945-4.588745.2145
96.94632.951-4.3832.0387-2.73914.99770.2444-0.10660.95110.3452-0.04240.4325-0.355-0.8312-0.27810.4679-0.08660.0610.5387-0.16380.5098-28.01464.235845.8549
102.7377-0.26251.24731.7108-0.24623.14020.0589-1.27350.29220.3022-0.11770.3406-0.005-1.13340.06850.6497-0.23840.16291.0265-0.17290.5024-35.7335-3.352659.2882
113.0056-0.26020.98871.829-0.32822.08980.1873-0.0813-0.618-0.2792-0.0545-0.0991.32930.1856-0.02791.3295-0.031-0.0590.47760.05350.583-8.4269-25.741353.9228
121.497-1.5756-0.26134.46351.04284.8148-0.5928-1.42220.61360.80660.3696-0.1608-0.6494-0.73690.04790.8646-0.0095-0.03681.4721-0.32230.5913-29.16191.332579.4133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 251 through 308 )A251 - 308
2X-RAY DIFFRACTION2chain 'A' and (resid 309 through 416 )A309 - 416
3X-RAY DIFFRACTION3chain 'A' and (resid 417 through 523 )A417 - 523
4X-RAY DIFFRACTION4chain 'A' and (resid 524 through 551 )A524 - 551
5X-RAY DIFFRACTION5chain 'A' and (resid 552 through 659 )A552 - 659
6X-RAY DIFFRACTION6chain 'A' and (resid 660 through 746 )A660 - 746
7X-RAY DIFFRACTION7chain 'B' and (resid 245 through 288 )B245 - 288
8X-RAY DIFFRACTION8chain 'B' and (resid 289 through 387 )B289 - 387
9X-RAY DIFFRACTION9chain 'B' and (resid 388 through 416 )B388 - 416
10X-RAY DIFFRACTION10chain 'B' and (resid 417 through 523 )B417 - 523
11X-RAY DIFFRACTION11chain 'B' and (resid 524 through 659 )B524 - 659
12X-RAY DIFFRACTION12chain 'B' and (resid 660 through 746 )B660 - 746

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