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- PDB-6kab: Crystal structure of plasmodium lysyl-tRNA synthetase in complex ... -

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Basic information

Entry
Database: PDB / ID: 6kab
TitleCrystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 2
ComponentsLysine--tRNA ligase
KeywordsLIGASE / Inhibitor / Complex
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / nucleic acid 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 / 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
Chem-D4U / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.892 Å
AuthorsZhou, J. / Fang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)21778064 China
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase.
Authors: Zhou, J. / Zheng, L. / Hei, Z. / Li, W. / Wang, J. / Yu, B. / Fang, P.
History
DepositionJun 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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

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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)240,81912
Polymers239,1254
Non-polymers1,6948
Water7,422412
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4096
Polymers119,5622
Non-polymers8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-45 kcal/mol
Surface area39320 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4096
Polymers119,5622
Non-polymers8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-45 kcal/mol
Surface area38850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.045, 90.008, 100.619
Angle α, β, γ (deg.)76.430, 72.920, 79.760
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 59781.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate NF54) (eukaryote)
Strain: isolate NF54 / Gene: PFNF54_04763 / Production host: Escherichia coli (E. coli) / References: UniProt: W7JP72, lysine-tRNA ligase
#2: Chemical
ChemComp-D4U / (3~{S})-3-(cyclohexylmethyl)-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one


Mass: 276.328 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: tri-sodium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 48151 / % possible obs: 94.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 38.94 Å2 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.079 / Rrim(I) all: 0.153 / Χ2: 0.508 / Net I/σ(I): 3.1 / Num. measured all: 176448
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-33.60.4348300.8620.2580.5030.4595.1
3-3.123.60.35748060.8930.2120.4160.4794.1
3.12-3.273.50.26244870.9340.1610.3080.49787.6
3.27-3.443.70.22149380.8520.1340.2590.49496.9
3.44-3.653.80.16849570.9430.1010.1970.53197.6
3.65-3.943.70.13149910.9710.0790.1530.5496.9
3.94-4.333.70.10148280.9890.060.1180.5695.1
4.33-4.963.60.08245680.9920.050.0960.57489.3
4.96-6.243.80.08949830.9910.0530.1040.47297.7
6.24-503.70.06547630.9940.0390.0760.49893.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YCV

4ycv


Resolution: 2.892→46.173 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 2423 5.04 %
Rwork0.224 45646 -
obs0.2265 48069 93.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.29 Å2 / Biso mean: 39.7014 Å2 / Biso min: 18.71 Å2
Refinement stepCycle: final / Resolution: 2.892→46.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15729 0 80 412 16221
Biso mean--26.28 27.95 -
Num. residues----2012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8916-2.9950.34032340.27674280451488
2.995-3.11490.32662470.26524595484294
3.1149-3.25660.31562050.26044309451488
3.2566-3.42820.28132620.23924685494796
3.4282-3.6430.28262710.22084740501197
3.643-3.92410.26992500.21694781503197
3.9241-4.31870.25762540.20054608486295
4.3187-4.9430.23462200.19214379459989
4.943-6.22530.2692550.2224777503298
6.2253-46.17890.25182250.22434492471792
Refinement TLS params.Method: refined / Origin x: 1.4573 Å / Origin y: 13.0438 Å / Origin z: 22.7589 Å
111213212223313233
T0.1804 Å2-0.0225 Å20.0273 Å2-0.2646 Å20.0268 Å2--0.264 Å2
L0.0868 °2-0.0024 °20.0735 °2-0.2311 °20.1638 °2--0.4023 °2
S-0.0015 Å °0.0052 Å °-0.0065 Å °-0.0058 Å °-0.0097 Å °0.0098 Å °-0.0116 Å °-0.0007 Å °0.0143 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA78 - 583
2X-RAY DIFFRACTION1allB79 - 582
3X-RAY DIFFRACTION1allC78 - 582
4X-RAY DIFFRACTION1allD78 - 582
5X-RAY DIFFRACTION1allS1 - 992
6X-RAY DIFFRACTION1allE1 - 4
7X-RAY DIFFRACTION1allK1 - 4

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