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- PDB-8w7l: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme P... -

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Basic information

Entry
Database: PDB / ID: 8w7l
TitleCryo-EM structure of ClassIII Lanthipeptide modification enzyme PneKC mutant H522A.
Components
  • (PneA) x 2
  • (Protein kinase domain-containing protein) x 2
KeywordsANTIMICROBIAL PROTEIN / Lanthibiotic / RiPPs / LanKC / CryoEM / Antimicrobial peptides / Antiviral peptides.
Function / homology
Function and homology information


peptide modification / protein kinase activity / ATP binding
Similarity search - Function
Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / : / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Protein kinase domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsLi, Y. / Luo, M. / Shao, K. / Li, J. / Li, Z.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Structure of PneA bound PneKC at 3.75 Angstroms resolution.
Authors: Li, Y. / Luo, M. / Shao, K. / Li, J. / Li, Z.
History
DepositionAug 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 2.0Nov 6, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / em_entity_assembly / em_imaging / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_ls_restr / struct_asym / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_admin.last_update / _em_entity_assembly.entity_id_list ..._em_admin.last_update / _em_entity_assembly.entity_id_list / _em_imaging.microscope_model / _pdbx_entity_nonpoly.entity_id / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_assembly.details / _pdbx_struct_oper_list.symmetry_operation / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _struct_asym.entity_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Description: Model completeness
Details: To correct residue placement and remove models exhibiting ambiguous electron density, ensuring higher accuracy and structural clarity.
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: Protein kinase domain-containing protein
B: Protein kinase domain-containing protein
C: PneA
D: PneA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,1026
Polymers203,9124
Non-polymers1902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein kinase domain-containing protein


Mass: 100104.680 Da / Num. of mol.: 1 / Mutation: H522A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SPRM200_1177 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U3S0J5
#2: Protein Protein kinase domain-containing protein


Mass: 99976.547 Da / Num. of mol.: 1 / Mutation: H522A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SPRM200_1177 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U3S0J5
#3: Protein/peptide PneA


Mass: 1972.220 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide PneA


Mass: 1858.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Production host: Escherichia coli (E. coli)
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dimeric structure of Class III lanthipeptide modification enzyme PneKC H522A in complex with substrate PneA
Type: COMPLEX / Entity ID: #1, #3 / Source: RECOMBINANT
Molecular weightValue: 0.21 MDa / Experimental value: YES
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4 / Details: 25mM Tris, 200mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMsodium chlorideNaCl1
225 mMTris(HOCH2)3CNH21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26420 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413905
ELECTRON MICROSCOPYf_angle_d0.98318908
ELECTRON MICROSCOPYf_dihedral_angle_d5.5451892
ELECTRON MICROSCOPYf_chiral_restr0.062088
ELECTRON MICROSCOPYf_plane_restr0.0062422

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