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- PDB-5elo: Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium p... -

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Basic information

Entry
Database: PDB / ID: 5elo
TitleCrystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and cladosporin
ComponentsLysine--tRNA ligase
Keywordsligase/ligase inhibitor / SSGCID / Lysine--tRNA ligase / Cryptosporidium parvum / ATP binding / aminoacylation / cladosporin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / ligase-ligase inhibitor complex
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / ATP binding / membrane / cytosol
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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...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 / 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) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
cladosporin / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis.
Authors: Baragana, B. / Forte, B. / Choi, R. / Nakazawa Hewitt, S. / Bueren-Calabuig, J.A. / Pisco, J.P. / Peet, C. / Dranow, D.M. / Robinson, D.A. / Jansen, C. / Norcross, N.R. / Vinayak, S. / ...Authors: Baragana, B. / Forte, B. / Choi, R. / Nakazawa Hewitt, S. / Bueren-Calabuig, J.A. / Pisco, J.P. / Peet, C. / Dranow, D.M. / Robinson, D.A. / Jansen, C. / Norcross, N.R. / Vinayak, S. / Anderson, M. / Brooks, C.F. / Cooper, C.A. / Damerow, S. / Delves, M. / Dowers, K. / Duffy, J. / Edwards, T.E. / Hallyburton, I. / Horst, B.G. / Hulverson, M.A. / Ferguson, L. / Jimenez-Diaz, M.B. / Jumani, R.S. / Lorimer, D.D. / Love, M.S. / Maher, S. / Matthews, H. / McNamara, C.W. / Miller, P. / O'Neill, S. / Ojo, K.K. / Osuna-Cabello, M. / Pinto, E. / Post, J. / Riley, J. / Rottmann, M. / Sanz, L.M. / Scullion, P. / Sharma, A. / Shepherd, S.M. / Shishikura, Y. / Simeons, F.R.C. / Stebbins, E.E. / Stojanovski, L. / Straschil, U. / Tamaki, F.K. / Tamjar, J. / Torrie, L.S. / Vantaux, A. / Witkowski, B. / Wittlin, S. / Yogavel, M. / Zuccotto, F. / Angulo-Barturen, I. / Sinden, R. / Baum, J. / Gamo, F.J. / Maser, P. / Kyle, D.E. / Winzeler, E.A. / Myler, P.J. / Wyatt, P.G. / Floyd, D. / Matthews, D. / Sharma, A. / Striepen, B. / Huston, C.D. / Gray, D.W. / Fairlamb, A.H. / Pisliakov, A.V. / Walpole, C. / Read, K.D. / Van Voorhis, W.C. / Gilbert, I.H.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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

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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)248,23319
Polymers245,8364
Non-polymers2,39715
Water35,4721969
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,0859
Polymers122,9182
Non-polymers1,1677
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-86 kcal/mol
Surface area38390 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,14710
Polymers122,9182
Non-polymers1,2298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-86 kcal/mol
Surface area38690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.220, 120.720, 143.330
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 61459.094 Da / Num. of mol.: 4 / Fragment: CrpaA.00612.a.A3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd4_2370 / Plasmid: CrpaA.00612.a.A3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5CR27, lysine-tRNA ligase

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Non-polymers , 5 types, 1984 molecules

#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-KRS / cladosporin / (3R)-3-[[(2R,6S)-6-methyloxan-2-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one


Mass: 292.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20O5
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1969 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: CrpaA.00612.a.A3.PW37710 at 35 mg/ml, protein was incubated with 3 mM MgCl2, L-lysine, and AMPPNP, then mixed 1:1 with Index(g5): 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris base/ ...Details: CrpaA.00612.a.A3.PW37710 at 35 mg/ml, protein was incubated with 3 mM MgCl2, L-lysine, and AMPPNP, then mixed 1:1 with Index(g5): 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris base/ HCl, pH = 8.5. Crystals were then soaked in a solution that was the previous crystallizaiton condition suplemented with 3 mM lysine and 2 mM cladopsorin for 24 hours, then cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 194875 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 20.97 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.98
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.84 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ELN

5eln


Resolution: 1.9→47.07 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 1994 1.02 %
Rwork0.204 --
obs0.204 194872 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15928 0 158 1969 18055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116648
X-RAY DIFFRACTIONf_angle_d1.06622550
X-RAY DIFFRACTIONf_dihedral_angle_d14.75510079
X-RAY DIFFRACTIONf_chiral_restr0.062434
X-RAY DIFFRACTIONf_plane_restr0.0072911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8999-1.94750.36671390.301613784X-RAY DIFFRACTION100
1.9475-2.00010.28991420.278413746X-RAY DIFFRACTION100
2.0001-2.0590.31581440.244913799X-RAY DIFFRACTION100
2.059-2.12540.30121450.236413728X-RAY DIFFRACTION100
2.1254-2.20140.29711420.230913859X-RAY DIFFRACTION100
2.2014-2.28950.29231420.238613755X-RAY DIFFRACTION100
2.2895-2.39370.26041410.217413740X-RAY DIFFRACTION100
2.3937-2.51990.29451400.215313801X-RAY DIFFRACTION100
2.5199-2.67780.25111460.217613720X-RAY DIFFRACTION99
2.6778-2.88450.27391450.218313727X-RAY DIFFRACTION99
2.8845-3.17470.23691380.204613750X-RAY DIFFRACTION99
3.1747-3.6340.2311450.184213711X-RAY DIFFRACTION99
3.634-4.57780.20561400.16313824X-RAY DIFFRACTION99
4.5778-47.08080.18331450.166913934X-RAY DIFFRACTION99
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)
11.0873-0.32080.00421.3214-0.48181.4530.33970.3696-0.1109-0.5359-0.4718-0.29930.17980.40480.06540.33530.14730.03960.27620.00820.13423.12529.198-21.294
21.831-1.2578-0.53251.4586-0.17131.25090.1070.06110.1896-0.1959-0.1038-0.31770.14090.23880.03520.15720.0049-0.00420.1245-0.0030.162210.62851.871-17.98
31.088-0.29210.53370.8876-0.15550.85980.11420.15830.0626-0.2605-0.05040.14-0.0544-0.0066-0.05230.18030.0372-0.03320.10680.00560.1119-12.94162.839-21.932
42.3758-0.93470.48241.7871-0.06911.2183-0.0212-0.08020.0866-0.12550.0533-0.3686-0.08410.121-0.03310.17220.00270.00630.1682-0.05720.15832.94664.695-2.124
50.8565-0.38140.30871.3794-0.30531.0915-0.11630.030.2387-0.04390.0611-0.1628-0.35150.04410.03870.2508-0.0185-0.00180.1484-0.0230.1345-8.182.226-11.895
61.4517-0.29480.17981.0215-0.01110.4840.08440.14460.3985-0.1526-0.0464-0.0917-0.0905-0.0536-0.05180.18870.01490.00150.13210.02530.1264-7.03366.146-18.366
71.5248-0.275-0.08891.53480.12321.1759-0.0504-0.3648-0.25610.11760.0030.5186-0.0133-0.32050.04910.11850.03060.02940.40.03150.3679-38.1564.233-3.741
81.3212-0.51060.43890.8896-0.25840.30410.29170.203-0.179-0.4059-0.15860.22620.13720.0619-0.11230.27310.057-0.05160.1639-0.01140.1135-6.01748.48-26.053
90.90140.169-0.59520.30640.48221.90260.1370.2888-0.4049-0.3056-0.140.27160.185-0.1967-0.03090.44820.1127-0.14990.2934-0.06290.3699-12.50829.442-36.733
101.0035-0.5982-0.09010.66170.00360.06770.45710.8634-0.185-0.6371-0.33650.34230.29570.06140.05290.51310.1998-0.09980.337-0.05780.1073-5.87142.159-33.658
111.1190.8313-0.2761.2965-0.29610.40620.1845-0.20110.04860.2577-0.1766-0.1899-0.12630.1647-0.02470.1496-0.0326-0.01890.2086-0.01490.167120.148-0.415-51.52
120.92650.3944-0.09140.684-0.03020.92610.00580.0499-0.16670.07880.0088-0.05160.17370.021-0.01160.1182-0.0049-0.01060.13020.0010.1437-7.881-36.77-57.248
131.65630.62230.15471.19610.48441.1045-0.06980.30890.2408-0.10190.04960.4111-0.0347-0.30220.0710.1195-0.0136-0.02870.39010.05410.3592-37.842-28.712-68.043
140.82290.0990.19390.82640.24930.37710.1234-0.26280.25810.2842-0.11170.18530.0179-0.0865-0.01920.2301-0.07680.06740.2412-0.04470.209-7.438-4.169-38.423
154.05612.61481.80473.24261.71882.69830.2055-0.54190.9825-0.34170.14280.5488-0.02020.362-0.36510.3666-0.05660.02940.1327-0.0370.1926-3.39-5.902-39.707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:179 )A44 - 179
2X-RAY DIFFRACTION2( CHAIN A AND RESID 180:232 )A180 - 232
3X-RAY DIFFRACTION3( CHAIN A AND RESID 233:318 )A233 - 318
4X-RAY DIFFRACTION4( CHAIN A AND RESID 319:354 )A319 - 354
5X-RAY DIFFRACTION5( CHAIN A AND RESID 355:491 )A355 - 491
6X-RAY DIFFRACTION6( CHAIN A AND ( RESID 492:545 OR RESID 601:601 ) )A492 - 545
7X-RAY DIFFRACTION6( CHAIN A AND ( RESID 492:545 OR RESID 601:601 ) )A601
8X-RAY DIFFRACTION7( CHAIN B AND RESID 45:209 )B45 - 209
9X-RAY DIFFRACTION8( CHAIN B AND RESID 210:318 )B210 - 318
10X-RAY DIFFRACTION9( CHAIN B AND RESID 319:454 )B319 - 454
11X-RAY DIFFRACTION10( CHAIN B AND ( RESID 455:545 OR RESID 601:601 ) )B455 - 545
12X-RAY DIFFRACTION10( CHAIN B AND ( RESID 455:545 OR RESID 601:601 ) )B601
13X-RAY DIFFRACTION11( CHAIN C AND RESID 45:232 )C45 - 232
14X-RAY DIFFRACTION12( CHAIN C AND ( RESID 233:544 OR RESID 601:601 ) )C233 - 544
15X-RAY DIFFRACTION12( CHAIN C AND ( RESID 233:544 OR RESID 601:601 ) )C601
16X-RAY DIFFRACTION13( CHAIN D AND RESID 45:209 )D45 - 209
17X-RAY DIFFRACTION14( CHAIN D AND RESID 210:545 )D210 - 545
18X-RAY DIFFRACTION15( CHAIN D AND RESID 601:601 )D601

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