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- PDB-6agt: Crystal structure of PfKRS complexed with chromone inhibitor -

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Basic information

Entry
Database: PDB / ID: 6agt
TitleCrystal structure of PfKRS complexed with chromone inhibitor
ComponentsLysine--tRNA ligase
KeywordsLIGASE/INHIBITOR / KRS / CHROMONE INHIBITOR / AMINOACYLATION / ATP BINDING PROTEIN / LIGASE-INHIBITOR COMPLEX
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 / tRNA binding / ATP binding / cytosol / 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-9X0 / : / FORMIC ACID / LYSINE / MALONIC ACID / Lysine--tRNA ligase / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.953 Å
AuthorsYogavel, M. / Sharma, A. / Sharma, A. / Baragana, B. / Walpole, C.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1032548 United States
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
DepositionAug 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_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
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,29124
Polymers234,8284
Non-polymers2,46320
Water9,800544
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,63912
Polymers117,4142
Non-polymers1,22510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-61 kcal/mol
Surface area39240 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,65212
Polymers117,4142
Non-polymers1,23810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-67 kcal/mol
Surface area38700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.761, 104.336, 100.594
Angle α, β, γ (deg.)89.880, 69.570, 61.100
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 58706.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFNF54_04763 / Production host: Escherichia coli (E. coli)
References: UniProt: W7JP72, UniProt: Q8IDJ8*PLUS, lysine-tRNA ligase

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Non-polymers , 6 types, 564 molecules

#2: Chemical
ChemComp-9X0 / N-(cyclohexylmethyl)-4-oxo-4H-1-benzopyran-2-carboxamide


Mass: 285.338 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H19NO3
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#6: Chemical
ChemComp-LYS / LYSINE


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


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M Bis-Tris pH 6.5, 2%(v/v) Tascimate pH 6.0, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97373 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 166896 / % possible obs: 96.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 28.65 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.041 / Rrim(I) all: 0.085 / Χ2: 1.326 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.984.40.60383830.9220.3230.6850.70396.8
1.98-2.024.40.44883330.9540.240.5090.71696.9
2.02-2.064.40.53983550.9010.2920.6141.01797
2.06-2.14.40.41483400.9270.2260.4721.2196.8
2.1-2.154.40.2983630.9660.1550.3290.83497.4
2.15-2.24.40.24884430.9770.1330.2820.87897.4
2.2-2.254.30.28982890.9590.1610.3321.9196.8
2.25-2.314.40.23284030.9820.1250.2641.09497.6
2.31-2.384.40.16684310.9880.0890.1891.0597.8
2.38-2.464.40.1584220.9880.0810.1711.16697.8
2.46-2.544.40.12884520.990.0690.1461.26797.9
2.54-2.654.40.11784130.9910.0630.1331.47798.1
2.65-2.774.40.10884610.990.0590.1231.66298.1
2.77-2.914.40.08184890.9940.0440.0921.68298.3
2.91-3.14.30.07584350.9940.0410.0861.75998.1
3.1-3.334.30.06484140.9950.0360.0731.88797.7
3.33-3.674.20.05883310.9960.0320.0671.84496.5
3.67-4.24.20.04981990.9960.0280.0571.69195
4.2-5.294.20.04481230.9970.0250.051.46494.6
5.29-504.10.03978170.9980.0220.0451.35190.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PG3

4pg3


Resolution: 1.953→31.902 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.52
RfactorNum. reflection% reflection
Rfree0.2432 8326 5.02 %
Rwork0.2027 --
obs0.2048 165823 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.97 Å2 / Biso mean: 45.64 Å2 / Biso min: 15.56 Å2
Refinement stepCycle: final / Resolution: 1.953→31.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15789 0 118 544 16451
Biso mean--36.66 38.15 -
Num. residues----1989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816765
X-RAY DIFFRACTIONf_angle_d1.15722691
X-RAY DIFFRACTIONf_chiral_restr0.0482447
X-RAY DIFFRACTIONf_plane_restr0.0062962
X-RAY DIFFRACTIONf_dihedral_angle_d14.2266324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9526-1.97480.33722520.27734973522591
1.9748-1.9980.30952770.27545332560997
1.998-2.02240.34192740.2675255552997
2.0224-2.0480.32312860.27545259554596
2.048-2.07490.39562720.3855187545995
2.0749-2.10330.33693060.28795185549196
2.1033-2.13340.30142750.24255380565597
2.1334-2.16520.2732600.23215266552697
2.1652-2.1990.26152790.23745386566597
2.199-2.23510.33832440.28545013525792
2.2351-2.27360.42092780.3734908518690
2.2736-2.31490.28312880.23445271555997
2.3149-2.35940.29192860.22795346563298
2.3594-2.40760.27622950.21855312560798
2.4076-2.45990.26522900.21795334562498
2.4599-2.51710.25122880.2175364565298
2.5171-2.580.25252980.21585302560098
2.58-2.64980.29852830.23915356563998
2.6498-2.72770.33152760.24185370564698
2.7277-2.81570.28032990.22545371567098
2.8157-2.91630.26212960.21555315561198
2.9163-3.03290.26482750.21995421569698
3.0329-3.17090.22662600.20935362562298
3.1709-3.33790.27462640.21355312557698
3.3379-3.54670.24092410.19815320556197
3.5467-3.82020.22682740.18355221549596
3.8202-4.20380.21292920.16375199549195
4.2038-4.81040.15262870.13345170545795
4.8104-6.05380.17112760.155083535993
6.0538-31.90620.18092550.15054924517990

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