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- PDB-7zog: Crystal structure of Cryptosporidium parvum -Plasmodium falciparu... -

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Basic information

Entry
Database: PDB / ID: 7zog
TitleCrystal structure of Cryptosporidium parvum -Plasmodium falciparum mutant lysyl tRNA synthetase in complex with inhibitor
ComponentsLysine-tRNA ligase
KeywordsLIGASE / tRNA binding
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / ATP binding / membrane / cytosol
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, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JE5 / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDawson, A. / Wyllie, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1193840 United States
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Toolkit of Approaches To Support Target-Focused Drug Discovery for Plasmodium falciparum Lysyl tRNA Synthetase.
Authors: Milne, R. / Wiedemar, N. / Corpas-Lopez, V. / Moynihan, E. / Wall, R.J. / Dawson, A. / Robinson, D.A. / Shepherd, S.M. / Smith, R.J. / Hallyburton, I. / Post, J.M. / Dowers, K. / Torrie, L.S. ...Authors: Milne, R. / Wiedemar, N. / Corpas-Lopez, V. / Moynihan, E. / Wall, R.J. / Dawson, A. / Robinson, D.A. / Shepherd, S.M. / Smith, R.J. / Hallyburton, I. / Post, J.M. / Dowers, K. / Torrie, L.S. / Gilbert, I.H. / Baragana, B. / Patterson, S. / Wyllie, S.
History
DepositionApr 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0Jun 19, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_unobs_or_zero_occ_atoms / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_ncs_dom_lim
Item: _entity.formula_weight / _entity.pdbx_description ..._entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][2] / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_percent_reflns_obs / _refine.pdbx_starting_model / _refine_hist.cycle_id / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _reflns.B_iso_Wilson_estimate / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_chi_squared / _reflns.percent_possible_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_chi_squared / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all / _struct_asym.entity_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id
Description: Ligand geometry
Details: I have (hopefully) repaired the bound lysine (Lys600) so that the OXT atom is included.
Provider: author / Type: Coordinate replacement

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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)249,81318
Polymers245,8564
Non-polymers3,95614
Water26,3921465
1
A: Lysine-tRNA ligase
B: Lysine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9069
Polymers122,9282
Non-polymers1,9787
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-48 kcal/mol
Surface area39330 Å2
2
C: Lysine-tRNA ligase
D: Lysine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9069
Polymers122,9282
Non-polymers1,9787
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-48 kcal/mol
Surface area39710 Å2
Unit cell
Length a, b, c (Å)73.103, 118.732, 143.454
Angle α, β, γ (deg.)90.00, 90.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA45 - 54421 - 520
21ARGARGBB45 - 54421 - 520
12LYSLYSAA - E45 - 60121
22LYSLYSCC - L45 - 60121
13LYSLYSAA - E45 - 60121
23LYSLYSDD - P45 - 60121
14ASNASNBB45 - 54521 - 521
24LYSLYSCC - L45 - 60121
15ASNASNBB45 - 54521 - 521
25LYSLYSDD - P45 - 60121
16LYSLYSCC - L45 - 60121
26LYSLYSDD - P45 - 60121

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 61464.109 Da / Num. of mol.: 4 / Mutation: P272T, N293V, A309S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Strain: Iowa II / Gene: cgd4_2370 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CR27, lysine-tRNA ligase
#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical
ChemComp-JE5 / 8-[[4-[2-[2-[2-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]sulfonylamino]-~{N}-(cyclohexylmethyl)-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide


Mass: 703.758 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H40FN6O9S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1465 / 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: 2.53 Å3/Da / Density % sol: 51.42 % / Description: rod
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: Reservoir: 0.1 M tris, pH 7.8, 0.2 M lithium sulfate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.8→64.9 Å / Num. obs: 226134 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.84 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1234 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALS3.4.3-1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HCW

6hcw


Resolution: 1.8→64.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.434 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.21 11382 5 %RANDOM
Rwork0.182 ---
obs0.183 214705 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.53 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å20 Å20.01 Å2
2--4.14 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→64.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15998 0 272 1465 17735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01316674
X-RAY DIFFRACTIONr_bond_other_d0.0020.01515732
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.64722465
X-RAY DIFFRACTIONr_angle_other_deg1.4051.59236434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96551964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41522.181885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07153005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.85615104
X-RAY DIFFRACTIONr_chiral_restr0.0760.22110
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218813
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023771
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A165330.05
12B165330.05
21A162150.05
22C162150.05
31A165820.06
32D165820.06
41B160740.05
42C160740.05
51B165740.05
52D165740.05
61C161830.06
62D161830.06
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 842 -
Rwork0.311 15841 -
obs--99.96 %

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