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- PDB-4pg3: Crystal structure of KRS complexed with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4pg3
TitleCrystal structure of KRS complexed with inhibitor
ComponentsLysine--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / Inhibitor / KRS / Complex / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / tRNA binding / ATP binding / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / 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, N-terminal / Lysine-tRNA ligase, class II / 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 speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.696 Å
AuthorsSharma, A. / Yogavel, M. / Khan, S. / Sharma, A. / Belrhali, H.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyPR6303 India
CitationJournal: 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
DepositionMay 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Non-polymer description
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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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)236,58612
Polymers234,8284
Non-polymers1,7588
Water4,810267
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2936
Polymers117,4142
Non-polymers8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-42 kcal/mol
Surface area39820 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2936
Polymers117,4142
Non-polymers8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-48 kcal/mol
Surface area39850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)297.913, 59.027, 141.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Fragment: UNP residues 77-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF13_0262 / Plasmid: PETM-41 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IDJ8, lysine-tRNA ligase
#2: Chemical
ChemComp-LYS / LYSINE / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris (6.5 pH), 2%v/v Tascimate (6.0 pH) and 20%w/v PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953725 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 2.696→30 Å / Num. obs: 69825 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 18.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H02

4h02


Resolution: 2.696→29.726 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 3412 5.05 %
Rwork0.193 --
obs0.1958 67595 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.696→29.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15495 0 124 267 15886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316222
X-RAY DIFFRACTIONf_angle_d0.66921953
X-RAY DIFFRACTIONf_dihedral_angle_d11.9946126
X-RAY DIFFRACTIONf_chiral_restr0.0262378
X-RAY DIFFRACTIONf_plane_restr0.0032829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6962-2.73460.35011190.26922049X-RAY DIFFRACTION76
2.7346-2.77540.31081140.25092255X-RAY DIFFRACTION83
2.7754-2.81880.34181190.23112387X-RAY DIFFRACTION87
2.8188-2.8650.29271420.24022495X-RAY DIFFRACTION93
2.865-2.91430.25451220.22852543X-RAY DIFFRACTION93
2.9143-2.96730.29381230.23282609X-RAY DIFFRACTION94
2.9673-3.02430.34261520.23572645X-RAY DIFFRACTION98
3.0243-3.08590.2981420.22222694X-RAY DIFFRACTION98
3.0859-3.1530.29631410.22042720X-RAY DIFFRACTION100
3.153-3.22620.27051400.21252747X-RAY DIFFRACTION100
3.2262-3.30680.28151450.21452765X-RAY DIFFRACTION100
3.3068-3.39610.24031450.20882720X-RAY DIFFRACTION100
3.3961-3.49590.25551520.21022781X-RAY DIFFRACTION100
3.4959-3.60850.24441380.19642731X-RAY DIFFRACTION100
3.6085-3.73730.2571350.19372777X-RAY DIFFRACTION100
3.7373-3.88660.21771520.17332758X-RAY DIFFRACTION100
3.8866-4.06310.21541220.17452776X-RAY DIFFRACTION100
4.0631-4.27670.22271580.16152792X-RAY DIFFRACTION100
4.2767-4.54380.17751550.14462772X-RAY DIFFRACTION100
4.5438-4.89320.21821630.14612773X-RAY DIFFRACTION100
4.8932-5.3830.23171530.16442800X-RAY DIFFRACTION100
5.383-6.15590.2421390.2012824X-RAY DIFFRACTION100
6.1559-7.73310.25021610.20972824X-RAY DIFFRACTION99
7.7331-29.72790.23821800.19062946X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -38.8157 Å / Origin y: 20.7379 Å / Origin z: -51.6922 Å
111213212223313233
T-0.006 Å20.1205 Å2-0.2256 Å2-0.0595 Å20.0133 Å2---0.0554 Å2
L0.023 °20.08 °2-0.0151 °2--0.1064 °20.0478 °2--0.1092 °2
S0.0433 Å °0.0067 Å °-0.0049 Å °0.0354 Å °-0.0654 Å °0.0314 Å °0.0987 Å °-0.028 Å °-0.0225 Å °
Refinement TLS groupSelection details: all

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