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- PDB-5zh5: CRYSTAL STRUCTURE OF PfKRS WITH INHIBITOR CLADO-2 -

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Basic information

Entry
Database: PDB / ID: 5zh5
TitleCRYSTAL STRUCTURE OF PfKRS WITH INHIBITOR CLADO-2
ComponentsLysine--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / KRS / LIGASE-LIGASE 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, 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
Chem-9CX / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum NF54 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.08 Å
AuthorsBabbar, P. / Malhotra, N. / Sharma, M. / Harlos, K. / Reddy, D.S. / Manickam, Y. / Sharma, A.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Specific Stereoisomeric Conformations Determine the Drug Potency of Cladosporin Scaffold against Malarial Parasite
Authors: Das, P. / Babbar, P. / Malhotra, N. / Sharma, M. / Jachak, G.R. / Gonnade, R.G. / Shanmugam, D. / Harlos, K. / Yogavel, M. / Sharma, A. / Reddy, D.S.
History
DepositionMar 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id

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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)118,3287
Polymers117,4142
Non-polymers9145
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-48 kcal/mol
Surface area39190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.500, 130.360, 174.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 77 - 601 / Label seq-ID: 1

Dom-IDAuth asym-IDLabel asym-ID
1AA - C
2BB - E

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Components

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


Mass: 58706.934 Da / Num. of mol.: 2 / Fragment: UNP residues 15-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum NF54 (eukaryote) / Gene: PFNF54_04763 / Plasmid: PETM11 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: W7JP72, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-9CX / (3S)-6,8-dihydroxy-3-{[(2R,6S)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one


Mass: 292.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20O5
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Carboxylic acids, 0.1M Sodium HEPES/MOPS, 25%(v/v) MPD; 25% PEG 1000; 25%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.08→42.17 Å / Num. obs: 23820 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Net I/σ(I): 9.25
Reflection shellResolution: 3.08→3.13 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.24 / Num. unique obs: 1153 / CC1/2: 0.6 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PG3

4pg3


Resolution: 3.08→42.17 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.887 / SU B: 72.432 / SU ML: 0.554 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.537 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1141 4.8 %RANDOM
Rwork0.243 ---
obs0.246 22625 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.51 Å2
Baniso -1Baniso -2Baniso -3
1-17.11 Å20 Å20 Å2
2---3.63 Å20 Å2
3----13.48 Å2
Refinement stepCycle: LAST / Resolution: 3.08→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7358 0 63 0 7421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197667
X-RAY DIFFRACTIONr_bond_other_d0.0040.027040
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.96910432
X-RAY DIFFRACTIONr_angle_other_deg1.0223.00216160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4375957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26324.235340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.545151194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5861535
X-RAY DIFFRACTIONr_chiral_restr0.0820.21165
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218700
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021768
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 26164 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.08→3.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 81 -
Rwork0.351 1625 -
obs--99.82 %
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)
10.8896-0.4195-0.25382.48510.91472.7025-0.09920.0305-0.42210.38190.0728-0.03680.72720.13680.02640.20570.01490.02960.6037-0.03680.879521.629-5.233-17.254
21.2363-1.0624-1.08162.43171.14273.2270.13580.4818-0.1754-0.5184-0.17120.18310.0893-0.21170.03540.1557-0.0301-0.02770.707-0.11170.7513.8027.771-37.784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A77 - 602
2X-RAY DIFFRACTION2B77 - 602

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