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- PDB-4wi1: Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA... -

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Basic information

Entry
Database: PDB / ID: 4wi1
TitleCrystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506
ComponentsProline--tRNA ligase
KeywordsLIGASE / SSGCID / Plasmodium falciparum / Prolyl-tRNA synthetase / ProRS / Proline--tRNA ligase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / aminoacyl-tRNA synthetase multienzyme complex / 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
Chem-3O6 / IMIDAZOLE / Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acs Infect Dis. / Year: 2016
Title: Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium falciparum Drug Target, Prolyl-tRNA-synthetase.
Authors: Nakazawa Hewitt, S. / 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. / ...Authors: Nakazawa Hewitt, S. / 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.S. / Stacy, R. / Barrett, L.K. / Gilbert, I.H. / Van Voorhis, W.C.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Derived calculations / Refinement description
Category: pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _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)119,83322
Polymers117,9732
Non-polymers1,86020
Water13,781765
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A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,94612
Polymers58,9861
Non-polymers96011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,88610
Polymers58,9861
Non-polymers9009
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)239,66544
Polymers235,9464
Non-polymers3,71940
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17130 Å2
ΔGint-17 kcal/mol
Surface area70660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.180, 91.340, 110.910
Angle α, β, γ (deg.)90.000, 129.530, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-809-

IMD

21A-963-

HOH

Detailsbiological unit is a monomer

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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: 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 , 6 types, 785 molecules

#2: Chemical ChemComp-3O6 / 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea


Mass: 396.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H13F5N4O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: at 21.9mg/ml, incubated with 5mM TCMDC-124506, then 1:1 with Morpheus(B2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each magnesium chloride, calcium chloride

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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-225 / Detector: CCD / Date: Sep 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 133468 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 21.93 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.056 / Χ2: 1.018 / Net I/σ(I): 16.31 / Num. measured all: 564551
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.65-1.694.20.8310.5393.01421541010897250.61596.2
1.69-1.740.8990.4033.9341245984895130.45996.6
1.74-1.790.9370.3144.8940141957592580.35896.7
1.79-1.840.9620.2336.3738971927989860.26696.8
1.84-1.910.9730.27.537920906787860.22996.9
1.91-1.970.9830.159.7435270871384560.17297.1
1.97-2.050.990.10912.4235457843482140.12497.4
2.05-2.130.9930.08814.9433998811579120.197.5
2.13-2.220.9950.07417.4632604780376220.08597.7
2.22-2.330.9950.06519.3329583742672350.07597.4
2.33-2.460.9960.05621.729669710369730.06498.2
2.46-2.610.9970.0524.2327863672566090.05798.3
2.61-2.790.9970.04726.0725865628661840.05398.4
2.79-3.010.9980.04228.4124285591158270.04898.6
3.01-3.30.9980.03830.8621800539453250.04498.7
3.3-3.690.9980.03732.5419615492648550.04298.6
3.69-4.260.9980.03433.7417327434242800.03998.6
4.26-5.220.9980.03234.214437368335930.03797.6
5.22-7.380.9980.0334.2411587288528240.03497.9
7.380.9980.0332.944760162512910.03579.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
ARPmodel building
PHENIX(phenix.refine: dev_1803)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q15

4q15


Resolution: 1.65→40.288 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 2133 1.6 %
Rwork0.1616 131328 -
obs0.162 133461 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.38 Å2 / Biso mean: 33.2662 Å2 / Biso min: 10.41 Å2
Refinement stepCycle: final / Resolution: 1.65→40.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7035 0 124 766 7925
Biso mean--41.95 40.9 -
Num. residues----875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077523
X-RAY DIFFRACTIONf_angle_d1.04710218
X-RAY DIFFRACTIONf_chiral_restr0.0441097
X-RAY DIFFRACTIONf_plane_restr0.0051298
X-RAY DIFFRACTIONf_dihedral_angle_d13.4262768
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 (%)
1.6499-1.68830.21031310.20148607873896
1.6883-1.73060.23121490.18518671882097
1.7306-1.77730.21851260.1828642876897
1.7773-1.82960.21931190.17658694881397
1.8296-1.88870.22041370.18668703884097
1.8887-1.95620.21881320.17918694882697
1.9562-2.03450.21481410.17498740888198
2.0345-2.12710.24511450.17468771891698
2.1271-2.23920.19711650.16868731889698
2.2392-2.37950.20411330.16658774890798
2.3795-2.56320.181460.16648893903999
2.5632-2.82110.1931560.16958833898999
2.8211-3.22920.19581410.17048929907099
3.2292-4.06780.17391620.14388909907199
4.0678-40.29990.15351500.14178737888796
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)
15.06012.67582.90833.36241.36383.3776-0.4597-0.23060.7597-0.22580.1830.3008-0.6128-0.01230.24380.35780.0150.00340.2105-0.07390.31641.538536.780739.9586
20.59830.41380.19151.77361.14572.01140.068-0.0780.1092-0.0221-0.03840.017-0.23250.0512-0.00140.1346-0.03780.00780.1387-0.01930.14414.187312.291421.6596
31.03930.1866-0.23111.16350.83151.85240.0564-0.06220.0199-0.0437-0.01020.0862-0.1113-0.0624-0.0420.1182-0.0162-0.02370.10560.01280.111-7.14664.717222.1547
41.37360.71780.6392.20251.44982.43910.05670.0466-0.170.16030.2056-0.41680.25430.3255-0.21960.21920.03-0.02170.2202-0.08680.252614.597125.947950.8946
54.28991.36312.43352.16911.26612.1560.1656-0.3046-0.22430.4926-0.1058-0.06070.3812-0.2785-0.05120.3326-0.05020.0370.2365-0.04020.1784-1.455815.086650.2601
60.76740.0912-0.34391.74260.15240.91950.42180.40740.764-0.3907-0.41170.6522-0.509-0.6636-0.00120.35510.19210.01970.5294-0.09540.6946-28.979418.313430.0691
71.1235-0.93240.41511.06610.36111.88940.34920.0870.3108-0.0575-0.45560.7509-0.1327-0.7399-0.05740.22340.06260.03750.4185-0.09580.5093-27.630711.775931.0997
81.41630.06480.58890.580.13451.83620.08130.01340.003-0.0699-0.055-0.0302-0.0280.1445-0.02060.1269-0.0373-0.01690.1302-0.00310.131816.74371.80848.5437
92.15491.43240.91342.4951.86511.57540.1374-0.12680.3413-0.17770.04380.0121-0.48270.170.07010.3465-0.13770.06770.2238-0.07270.251116.310424.097120.595
100.880.52890.0021.47320.27410.45360.1984-0.2360.2757-0.06430.0396-0.1754-0.36990.4361-0.16720.2917-0.21990.0840.2969-0.12190.291629.752319.936217.3078
111.0360.0373-0.00172.0753-0.932.2692-0.2131-0.2121-0.57050.3559-0.07380.41010.5533-0.11990.12310.317-0.0240.14970.23060.02040.399317.7038-18.15517.007
121.42711.2625-1.07863.0326-1.03751.6933-0.0086-0.1887-0.0879-0.0297-0.0408-0.5178-0.17380.28390.05230.1813-0.05590.02080.2977-0.03710.287840.74358.92576.6039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 242 through 272 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 273 through 370 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 371 through 523 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 524 through 620 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 621 through 659 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 660 through 695 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 696 through 746 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 250 through 308 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 309 through 416 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 417 through 523 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 524 through 620 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 621 through 746 )B0

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