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- PDB-6m0t: Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falcip... -

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Basic information

Entry
Database: PDB / ID: 6m0t
TitleCrystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin derivative (CL-2)
ComponentsLysine--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / Cladosporin analog / Stereochemistry / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


Transcriptional and post-translational regulation of MITF-M expression and activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / 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) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Chem-EZ3 / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsBabbar, P. / Sharma, A. / Manickam, Y.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR13636 India
Citation
Journal: Acs Infect Dis. / Year: 2021
Title: Design, Synthesis, and Structural Analysis of Cladosporin-Based Inhibitors of Malaria Parasites.
Authors: Babbar, P. / Das, P. / Manickam, Y. / Mankad, Y. / Yadav, S. / Parvez, S. / Sharma, A. / Reddy, D.S.
#1: Journal: J Struct Funct Genomics. / Year: 2014
Title: Structural basis of malaria parasite lysyl-tRNA synthetase inhibition by cladosporin.
Authors: Khan, S. / Sharma, A. / Belrhali, H. / Yogavel, M. / Sharma, A.
History
DepositionFeb 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,65012
Polymers234,8284
Non-polymers1,8228
Water2,054114
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3256
Polymers117,4142
Non-polymers9114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-43 kcal/mol
Surface area41080 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3256
Polymers117,4142
Non-polymers9114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-47 kcal/mol
Surface area41430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)299.560, 59.140, 141.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Lysine--tRNA ligase / Lysyl-tRNA synthetase


Mass: 58706.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1350100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IDJ8, lysine-tRNA ligase
#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical
ChemComp-EZ3 / (3R)-3-[(R)-[(2R,6S)-6-methyloxan-2-yl]-oxidanyl-methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one


Mass: 308.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Carboxylic acids,0.1 M Buffer System1 6.5- Imidazole and MES monohydrate, 50%v/v Precipitant Mix - 25% v/vMPD, 25% PEG 1000, 25% w/V PEG3350

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Data collection

DiffractionMean temperature: 293.14 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.68→36.841 Å / Num. obs: 72044 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.139 / Net I/σ(I): 12.6
Reflection shellResolution: 2.68→7.26 Å / Rmerge(I) obs: 1.664 / Num. unique obs: 3514 / CC1/2: 0.501

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PG3

4pg3


Resolution: 2.68→36.841 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.83
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2463 3505 4.87 %
Rwork0.1903 --
obs0.1931 71965 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 191.92 Å2 / Biso mean: 70 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.68→36.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15951 0 98 114 16163
Biso mean--57.8 55.77 -
Num. residues----1955
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.68-2.71670.39311320.32622669
2.7167-2.75550.35631200.31152696
2.7555-2.79660.35111340.29662742
2.7966-2.84030.3331390.25952685
2.8403-2.88690.36291210.24962696
2.8869-2.93660.30571380.24252729
2.9366-2.990.31271430.24022674
2.99-3.04750.28611350.24162686
3.0475-3.10970.29851390.24382772
3.1097-3.17720.34641450.22672648
3.1772-3.25110.27181280.22052746
3.2511-3.33240.30251460.21262702
3.3324-3.42240.25821550.20952702
3.4224-3.5230.24181050.20422746
3.523-3.63660.29041400.19832735
3.6366-3.76650.27511500.19482723
3.7665-3.91710.25561560.17742734
3.9171-4.09520.20721470.17232696
4.0952-4.31080.20861570.1572742
4.3108-4.58040.22391430.14512778
4.5804-4.93330.18411350.13712781
4.9333-5.42840.2431390.15572773
5.4284-6.21060.22751510.18462780
6.2106-7.81240.21681440.20072848
7.8124-36.8410.21051630.18672977
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)
12.2666-0.3065-0.12642.6589-0.50533.5364-0.18150.39810.3764-0.71310.0392-0.6258-0.52250.02010.14970.8951-0.23440.23860.5880.02190.5896-23.02629.221-10.214
24.837-2.1116-0.48053.8081-1.65693.938-0.44820.2868-0.10360.1260.237-0.16710.011-0.09430.16560.5408-0.21730.04020.5417-0.05250.446-42.6528.46414.035
31.691-0.20220.80040.6479-0.69491.5498-0.14070.5254-0.2474-0.4510.11510.0470.352-0.2360.05490.6958-0.20360.0520.6876-0.09640.3929-55.4231.31610.296
41.29050.3601-0.1140.7463-0.19270.0178-0.51040.6364-0.2747-0.42710.37370.06080.4537-0.32390.16440.8261-0.22650.08050.7694-0.13130.5294-55.758-3.01412.443
52.8747-0.9427-0.58324.627-0.10262.4257-0.0525-0.4533-0.23670.09940.04720.26550.1207-0.2799-0.02830.4380.01920.02940.51560.03960.3281-63.8547.45144.113
61.87220.3402-0.54711.2968-0.56221.1691-0.1688-0.0498-0.1901-0.06150.0328-0.1351-0.0604-0.00790.12430.4537-0.01380.0090.4167-0.08860.3365-45.6648.48533.486
71.9020.0452-0.35891.35070.17981.6159-0.2066-0.1762-0.14220.0267-0.0403-0.4988-0.00060.33780.15350.57-0.06820.11140.5459-0.0110.6392-17.52615.21622.567
81.85760.3894-1.55551.66450.02273.6246-0.2211-0.0552-0.1747-0.19710.0407-0.55710.04310.33250.22210.3749-0.06150.10180.4511-0.03410.5868-18.29115.53417.958
90.12070.1943-0.04730.3307-0.11561.73980.2409-0.17310.02630.1016-0.07730.271-0.0519-0.1755-0.16860.736-0.0580.01770.6631-0.21240.7121-41.7341.445-30.718
104.32576.7259-6.16482.0001-9.815320.7985-0.01610.07013.7932-2.18890.395-2.29062.05391.34490.8306-0.12180.09840.5425-0.15320.733-20.88714.07415.199
114.2029-0.8906-1.5014.4424-0.1523.62990.14020.12890.2541-0.4128-0.041-0.3421-0.64840.4313-0.07630.6376-0.09810.04710.50590.02360.3988-23.47928.694-81.546
127.33470.9341-1.6736.9969-0.67486.1101-0.67271.015-0.1277-1.18720.1613-0.02420.3302-0.25150.2910.4973-0.00830.10990.5053-0.09370.3659-30.2527.097-80.606
134.1398-2.41260.3782.3497-0.90365.1769-0.2309-0.3165-0.08770.46480.14970.0923-0.10420.0750.09230.3-0.0925-0.03550.3076-0.01210.3705-43.2593.324-57.174
141.1488-0.4053-0.53331.6238-0.4062.427-0.12770.1382-0.0089-0.077-0.04250.12640.2152-0.23330.15560.3836-0.00550.03790.4079-0.05450.3298-54.608-6.051-60.268
152.26441.1288-1.37073.32670.63774.9537-0.28790.1864-0.3360.03320.1101-0.22230.45840.06850.10830.3502-0.00050.03250.4849-0.07990.3799-57.837-14.441-57.37
162.49520.8034-2.41711.236-2.14356.8632-0.10410.05730.0237-0.0163-0.00560.09480.3162-0.21420.17830.47070.0076-0.00330.3454-0.09150.4537-46.027-2.609-59.083
171.61240.2018-0.94041.2402-0.57712.26240.061-0.2869-0.01950.4035-0.10010.1219-0.1443-0.21730.04890.5016-0.0179-0.00730.6107-0.06390.3827-55.7733.401-33.206
180.81310.2293-0.35030.89580.20591.3870.0655-0.3029-0.0940.2091-0.1533-0.3039-0.1070.62680.06570.4535-0.0526-0.04160.70860.04570.4985-19.71513.173-49.563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 80:244 )C80 - 244
2X-RAY DIFFRACTION2( CHAIN C AND RESID 245:294 )C245 - 294
3X-RAY DIFFRACTION3( CHAIN C AND RESID 295:435 )C295 - 435
4X-RAY DIFFRACTION4( CHAIN C AND RESID 436:581 )C436 - 581
5X-RAY DIFFRACTION5( CHAIN D AND RESID 80:176 )D80 - 176
6X-RAY DIFFRACTION6( CHAIN D AND RESID 177:294 )D177 - 294
7X-RAY DIFFRACTION7( CHAIN D AND RESID 295:456 )D295 - 456
8X-RAY DIFFRACTION8( CHAIN D AND RESID 457:581 )D457 - 581
9X-RAY DIFFRACTION9( CHAIN A AND RESID 601:601 ) OR ( CHAIN C AND RESID 601:601 ) OR ( CHAIN B AND RESID 601:601 )A601
10X-RAY DIFFRACTION9( CHAIN A AND RESID 601:601 ) OR ( CHAIN C AND RESID 601:601 ) OR ( CHAIN B AND RESID 601:601 )C601
11X-RAY DIFFRACTION9( CHAIN A AND RESID 601:601 ) OR ( CHAIN C AND RESID 601:601 ) OR ( CHAIN B AND RESID 601:601 )B601
12X-RAY DIFFRACTION10( CHAIN D AND RESID 601:601 )D601
13X-RAY DIFFRACTION11( CHAIN A AND RESID 80:215 )A80 - 215
14X-RAY DIFFRACTION12( CHAIN A AND RESID 216:244 )A216 - 244
15X-RAY DIFFRACTION13( CHAIN A AND RESID 245:294 )A245 - 294
16X-RAY DIFFRACTION14( CHAIN A AND RESID 295:434 )A295 - 434
17X-RAY DIFFRACTION15( CHAIN A AND RESID 435:536 )A435 - 536
18X-RAY DIFFRACTION16( CHAIN A AND RESID 537:581 )A537 - 581
19X-RAY DIFFRACTION17( CHAIN B AND RESID 80:294 )B80 - 294
20X-RAY DIFFRACTION18( CHAIN B AND RESID 295:581 )B295 - 581

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