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- PDB-7bt5: Crystal structure of plasmodium LysRS complexing with an antitumo... -

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Basic information

Entry
Database: PDB / ID: 7bt5
TitleCrystal structure of plasmodium LysRS complexing with an antitumor compound
ComponentsLysine--tRNA ligase
KeywordsLIGASE / protein translation / lysyl-tRNA synthetase
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 / nucleic acid binding / 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-F6O / LYSINE / Lysine--tRNA ligase / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å
AuthorsZhou, J. / Wang, J. / Fang, P.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778067 China
National Natural Science Foundation of China (NSFC)21778064 China
National Natural Science Foundation of China (NSFC)21977107 China
National Natural Science Foundation of China (NSFC)21977108 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Inhibition of Plasmodium falciparum Lysyl-tRNA synthetase via an anaplastic lymphoma kinase inhibitor.
Authors: Zhou, J. / Huang, Z. / Zheng, L. / Hei, Z. / Wang, Z. / Yu, B. / Jiang, L. / Wang, J. / Fang, P.
History
DepositionMar 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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 1.4Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0186
Polymers119,5622
Non-polymers1,4564
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-44 kcal/mol
Surface area39640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.749, 166.401, 70.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 78 through 80 or (resid 81...
21(chain B and (resid 78 through 96 or (resid 97...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 78 through 80 or (resid 81...A78 - 80
121(chain A and (resid 78 through 80 or (resid 81...A81 - 82
131(chain A and (resid 78 through 80 or (resid 81...A1 - 581
141(chain A and (resid 78 through 80 or (resid 81...A1 - 581
151(chain A and (resid 78 through 80 or (resid 81...A1 - 581
161(chain A and (resid 78 through 80 or (resid 81...A1 - 581
211(chain B and (resid 78 through 96 or (resid 97...B78 - 96
221(chain B and (resid 78 through 96 or (resid 97...B97
231(chain B and (resid 78 through 96 or (resid 97...B2 - 581
241(chain B and (resid 78 through 96 or (resid 97...B0
251(chain B and (resid 78 through 96 or (resid 97...B2 - 581
261(chain B and (resid 78 through 96 or (resid 97...B118
271(chain B and (resid 78 through 96 or (resid 97...B2 - 581
281(chain B and (resid 78 through 96 or (resid 97...B2 - 581
291(chain B and (resid 78 through 96 or (resid 97...B2 - 581
2101(chain B and (resid 78 through 96 or (resid 97...B2 - 581
2111(chain B and (resid 78 through 96 or (resid 97...B2 - 581
2121(chain B and (resid 78 through 96 or (resid 97...B2 - 581

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Components

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


Mass: 59781.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli)
References: UniProt: W7F9C1, UniProt: Q8IDJ8*PLUS, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-F6O / N4-[2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]-N2-(2-propan-2-ylsulfonylphenyl)-1,3,5-triazine-2,4-diamine


Mass: 580.745 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H40N8O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: MES pH 6.0, PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.49→84.28 Å / Num. obs: 41176 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 55.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.037 / Rrim(I) all: 0.101 / Net I/σ(I): 12.7 / Num. measured all: 299352
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.49-2.637.50.7324475759370.8520.2820.7852.7100
7.88-84.286.20.056888614410.9960.0240.06125.899.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YCV

4ycv


Resolution: 2.493→50 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.1
RfactorNum. reflection% reflection
Rfree0.2371 2005 4.88 %
Rwork0.2127 --
obs0.214 41090 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.99 Å2 / Biso mean: 68.0121 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.493→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7672 0 82 133 7887
Biso mean--58.54 57.26 -
Num. residues----969
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4331X-RAY DIFFRACTION10.183TORSIONAL
12B4331X-RAY DIFFRACTION10.183TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4934-2.58250.36951780.30393860100
2.5825-2.68590.31612000.26963854100
2.6859-2.80810.29642100.26173856100
2.8081-2.95620.31442140.26053855100
2.9562-3.14130.30741960.26253847100
3.1413-3.38380.28661980.23783915100
3.3838-3.72420.26632000.22413884100
3.7242-4.26280.22932020.19013923100
4.2628-5.36950.18371990.16843979100
5.3695-46.890.18452080.198411299
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)
10.71560.19270.10571.8216-0.35380.7381-0.07670.1336-0.0473-0.41640.09850.11530.0293-0.0051-0.02070.4398-0.0534-0.0450.4533-0.0350.3632-24.706329.3101-19.7839
20.82320.37940.0082.2469-0.59121.3070.0417-0.1121-0.04040.2724-0.07160.0042-0.2190.08510.02690.3325-0.0099-0.02130.442-0.01070.3288-22.458236.59224.9894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 78 through 581)A78 - 581
2X-RAY DIFFRACTION2(chain 'B' and resid 78 through 581)B78 - 581

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