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- PDB-7nbu: Structure of the HigB1 toxin mutant K95A from Mycobacterium tuber... -

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Basic information

Entry
Database: PDB / ID: 7nbu
TitleStructure of the HigB1 toxin mutant K95A from Mycobacterium tuberculosis (Rv1955) and its target, the cspA mRNA, on the E. coli Ribosome.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • E-site tRNA
  • P-site fMet-tRNA(fMet)
  • Probable endoribonuclease HigB1
  • cspA mRNA
KeywordsTOXIN
Function / homology
Function and homology information


detoxification / negative regulation of growth / negative regulation of cytoplasmic translational initiation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation ...detoxification / negative regulation of growth / negative regulation of cytoplasmic translational initiation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / four-way junction DNA binding / negative regulation of translational initiation / translation repressor activity / RNA endonuclease activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / Hydrolases; Acting on ester bonds / rRNA binding / response to hypoxia / molecular adaptor activity / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Toxin HigB-like / Phage derived protein Gp49-like (DUF891) / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site ...Toxin HigB-like / Phage derived protein Gp49-like (DUF891) / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20
Similarity search - Domain/homology
N-FORMYLMETHIONINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL16 / : ...N-FORMYLMETHIONINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL16 / : / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25 / Probable endoribonuclease HigB1 / Large ribosomal subunit protein bL9
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Escherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsGiudice, E. / Mansour, M. / Chat, S. / D'Urso, G. / Gillet, R. / Genevaux, P.
Funding support France, Switzerland, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE12-0026 France
Swiss National Science FoundationSNF CRSII3_160703 Switzerland
CitationJournal: Nat Commun / Year: 2022
Title: Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis.
Authors: Moise Mansour / Emmanuel Giudice / Xibing Xu / Hatice Akarsu / Patricia Bordes / Valérie Guillet / Donna-Joe Bigot / Nawel Slama / Gaetano D'urso / Sophie Chat / Peter Redder / Laurent ...Authors: Moise Mansour / Emmanuel Giudice / Xibing Xu / Hatice Akarsu / Patricia Bordes / Valérie Guillet / Donna-Joe Bigot / Nawel Slama / Gaetano D'urso / Sophie Chat / Peter Redder / Laurent Falquet / Lionel Mourey / Reynald Gillet / Pierre Genevaux /
Abstract: Toxins of toxin-antitoxin systems use diverse mechanisms to control bacterial growth. Here, we focus on the deleterious toxin of the atypical tripartite toxin-antitoxin-chaperone (TAC) system of ...Toxins of toxin-antitoxin systems use diverse mechanisms to control bacterial growth. Here, we focus on the deleterious toxin of the atypical tripartite toxin-antitoxin-chaperone (TAC) system of Mycobacterium tuberculosis, whose inhibition requires the concerted action of the antitoxin and its dedicated SecB-like chaperone. We show that the TAC toxin is a bona fide ribonuclease and identify exact cleavage sites in mRNA targets on a transcriptome-wide scale in vivo. mRNA cleavage by the toxin occurs after the second nucleotide of the ribosomal A-site codon during translation, with a strong preference for CCA codons in vivo. Finally, we report the cryo-EM structure of the ribosome-bound TAC toxin in the presence of native M. tuberculosis cspA mRNA, revealing the specific mechanism by which the TAC toxin interacts with the ribosome and the tRNA in the P-site to cleave its mRNA target.
History
DepositionJan 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_entity_assembly / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_polymer_linkage / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_entity_assembly.entity_id_list / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly_gen.asym_id_list / _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_atom_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Revision 2.1Mar 13, 2024Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 2.2Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

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Assembly

Deposited unit
A: 16S ribosomal RNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein S21
V: P-site fMet-tRNA(fMet)
W: E-site tRNA
X: cspA mRNA
Y: Probable endoribonuclease HigB1
a: 23S ribosomal RNA
b: 5S ribosomal RNA
c: 50S ribosomal protein L2
d: 50S ribosomal protein L3
e: 50S ribosomal protein L4
f: 50S ribosomal protein L5
g: 50S ribosomal protein L6
h: 50S ribosomal protein L9
i: 50S ribosomal protein L13
j: 50S ribosomal protein L14
k: 50S ribosomal protein L15
l: 50S ribosomal protein L16,50S ribosomal protein L31
Z: 50S ribosomal protein L16
m: 50S ribosomal protein L17
n: 50S ribosomal protein L18
o: 50S ribosomal protein L19
p: 50S ribosomal protein L20
q: 50S ribosomal protein L21
r: 50S ribosomal protein L22
s: 50S ribosomal protein L23
t: 50S ribosomal protein L24
u: 50S ribosomal protein L25
v: 50S ribosomal protein L27
w: 50S ribosomal protein L28
x: 50S ribosomal protein L29
y: 50S ribosomal protein L30
z: 50S ribosomal protein L32
0: 50S ribosomal protein L33
1: 50S ribosomal protein L34
2: 50S ribosomal protein L35
3: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,155,043372
Polymers2,147,12856
Non-polymers7,916316
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 6 types, 6 molecules AVWXab

#1: RNA chain 16S ribosomal RNA /


Mass: 498846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB U000096.3 545778205 223771-225312 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 817573384
#22: RNA chain P-site fMet-tRNA(fMet)


Mass: 24818.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 731469900
#23: RNA chain E-site tRNA


Mass: 589.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: Mre 600
#24: RNA chain cspA mRNA


Mass: 3144.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: rv3648c (cspA)
Source: (natural) Mycobacterium tuberculosis H37Rv (bacteria)
#26: RNA chain 23S ribosomal RNA /


Mass: 941822.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB U000096.3 545778205 225759 - 228662 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MG1655
#27: RNA chain 5S ribosomal RNA /


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB U000096.3 545778205 228756 - 228875 / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 1845258627

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30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S ribosomal protein S2 / / Small ribosomal subunit protein uS2


Mass: 24971.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7V0 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7V0
#3: Protein 30S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7V3 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7V3
#4: Protein 30S ribosomal protein S4 / / Small ribosomal subunit protein uS4


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7V8 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7V8
#5: Protein 30S ribosomal protein S5 / / Small ribosomal subunit protein uS5


Mass: 16475.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7W1 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7W1
#6: Protein 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 11996.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P02358 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P02358
#7: Protein 30S ribosomal protein S7 /


Mass: 17162.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P02359 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: A0A4S5AV58
#8: Protein 30S ribosomal protein S8 / / Small ribosomal subunit protein uS8


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7W7 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7W7
#9: Protein 30S ribosomal protein S9 / / Small ribosomal subunit protein uS9


Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7X3 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7X3
#10: Protein 30S ribosomal protein S10 / / Small ribosomal subunit protein uS10


Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7R5 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7R5
#11: Protein 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


Mass: 12488.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7R9 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7R9
#12: Protein 30S ribosomal protein S12 / / Small ribosomal subunit protein uS12


Mass: 13683.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7S3 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7S3
#13: Protein 30S ribosomal protein S13 / / Small ribosomal subunit protein uS13


Mass: 12738.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7S9 / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7S9
#14: Protein 30S ribosomal protein S14 / / Small ribosomal subunit protein uS14


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0AG59 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG59
#15: Protein 30S ribosomal protein S15 / / Small ribosomal subunit protein uS15


Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0ADZ4 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0ADZ4
#16: Protein 30S ribosomal protein S16 / / Small ribosomal subunit protein bS16


Mass: 9136.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7T3 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7T3
#17: Protein 30S ribosomal protein S17 / / Small ribosomal subunit protein uS17


Mass: 9164.815 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0AG63 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG63
#18: Protein 30S ribosomal protein S18 / / Small ribosomal subunit protein bS18


Mass: 7735.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7T7 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7T7
#19: Protein 30S ribosomal protein S19 / / Small ribosomal subunit protein uS19


Mass: 9492.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7U3 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7U3
#20: Protein 30S ribosomal protein S20 / / Small ribosomal subunit protein bS20


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7U7 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7U7
#21: Protein 30S ribosomal protein S21 / / Small ribosomal subunit protein bS21


Mass: 8392.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P68679 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P68679

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Protein , 1 types, 1 molecules Y

#25: Protein Probable endoribonuclease HigB1 / Toxin HigB1


Mass: 14003.255 Da / Num. of mol.: 1 / Mutation: K95A
Source method: isolated from a genetically manipulated source
Details: P9WJA5
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: higB1, higB, Rv1955 / Plasmid: pET20b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): AI
References: UniProt: P9WJA5, Hydrolases; Acting on ester bonds

+
50S ribosomal protein ... , 29 types, 29 molecules cdefghijklZmnopqrstuvwxyz0123

#28: Protein 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P60422 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P60422
#29: Protein 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22291.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P60438 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P60438
#30: Protein 50S ribosomal protein L4 / / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P60723 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P60723
#31: Protein 50S ribosomal protein L5 / / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P62399 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P62399
#32: Protein 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18801.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0AG55 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG55
#33: Protein/peptide 50S ribosomal protein L9 /


Mass: 4330.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7R1 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: Q328J6
#34: Protein 50S ribosomal protein L13 / / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0AA10 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AA10
#35: Protein 50S ribosomal protein L14 / / Large ribosomal subunit protein uL14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0ADY3 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0ADY3
#36: Protein 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P02413 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P02413
#37: Protein 50S ribosomal protein L16,50S ribosomal protein L31 / Ribosome / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL31-A


Mass: 16900.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0ADY7, P0A7M9,P0ADY7, P0A7M9 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0ADY7, UniProt: P0A7M9
#38: Protein 50S ribosomal protein L16 /


Mass: 5946.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0ADY7 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: A0A3S4NPI3
#39: Protein 50S ribosomal protein L17 / / Large ribosomal subunit protein bL17


Mass: 13505.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0AG44 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG44
#40: Protein 50S ribosomal protein L18 / / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0C018 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0C018
#41: Protein 50S ribosomal protein L19 / / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7K6 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7K6
#42: Protein 50S ribosomal protein L20 / / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7L3 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7L3
#43: Protein 50S ribosomal protein L21 / / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0AG48 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG48
#44: Protein 50S ribosomal protein L22 / / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P61175 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P61175
#45: Protein 50S ribosomal protein L23 / / Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0ADZ0 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0ADZ0
#46: Protein 50S ribosomal protein L24 / / Large ribosomal subunit protein uL24


Mass: 11078.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P60624 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P60624
#47: Protein 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P68919 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P68919
#48: Protein 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 9015.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7L8 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7L8
#49: Protein 50S ribosomal protein L28 / / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7M2 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7M2
#50: Protein 50S ribosomal protein L29 / / Large ribosomal subunit protein uL29


Mass: 7155.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7M6 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7M6
#51: Protein 50S ribosomal protein L30 / / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0AG51 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG51
#52: Protein 50S ribosomal protein L32 / / Large ribosomal subunit protein bL32


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7N4 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7N4
#53: Protein 50S ribosomal protein L33 / / Large ribosomal subunit protein bL33


Mass: 5928.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7N9 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7N9
#54: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7P5 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7P5
#55: Protein 50S ribosomal protein L35 / / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7Q1 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7Q1
#56: Protein/peptide 50S ribosomal protein L36 / / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7Q6 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7Q6

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Non-polymers , 3 types, 316 molecules

#57: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 313 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-FME / N-FORMYLMETHIONINE / N-Formylmethionine


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S
#59: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN

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Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1M. tuberculosis HigB1_K95A mutant toxin and its target, the CspA mRNA, on the E. coli Ribosome.RIBOSOME#1-#36, #39-#560MULTIPLE SOURCES
230S Ribosomal subunitProkaryotic small ribosomal subunitCOMPLEX#1-#211NATURAL
350S Ribosomal subunitProkaryotic large ribosomal subunitCOMPLEX#26-#36, #39-#561NATURAL
416S rRNACOMPLEX#12NATURAL
530S ribosomal proteinsRibosomal proteinCOMPLEX#2-#212NATURAL
623S and 5S rRNACOMPLEX#26-#273NATURAL
750S ribosomal proteinsRibosomal proteinCOMPLEX#28-#36, #39-#563NATURAL
8P-site fMet-tRNA(fMet)COMPLEX#221MULTIPLE SOURCES
9E-site tRNACOMPLEX#231MULTIPLE SOURCES
10cspA mRNACOMPLEX#241MULTIPLE SOURCES
11HigB1 toxinCOMPLEX#251RECOMBINANTK95A inactive mutant
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
41NO
51NO
61NO
71NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Escherichia coli K-12 (bacteria)83333MG1655
22Escherichia coli K-12 (bacteria)83333MG1655
33Escherichia coli K-12 (bacteria)83333MG1655
54Escherichia coli K-12 (bacteria)83333MG1655
55Escherichia coli K-12 (bacteria)83333MG1655
76Escherichia coli K-12 (bacteria)83333MG1655
77Escherichia coli K-12 (bacteria)83333MG1655
88Escherichia coli K-12 (bacteria)83333MG1655
99Escherichia coli K-12 (bacteria)83333MG1655
1010Escherichia coli K-12 (bacteria)83333MG1655
1111Mycobacterium tuberculosis (bacteria)1773ATCC 25618 / H37Rv
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
15 mMHEPES-KOHC8H19N2O5SK1
250 mMKCLKCl1
310 mMMgOAcMgOAc1
410 mMNH4ClNH4Cl1
51 mMDithiothreitolC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K / Details: blot for 2s before plunging

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90 K / Temperature (min): 90 K
Image recordingAverage exposure time: 6.5 sec. / Electron dose: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6381
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 65 / Used frames/image: 1-65

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimera1.13.1model fitting
9RELION3.1initial Euler assignmentbeta-commit-c17c89
10RELION3.1final Euler assignmentbeta-commit-c17c89
11RELION3.1classificationbeta-commit-c17c89
12RELION3.13D reconstructionbeta-commit-c17c89
19PHENIX1.18.2-3874model refinement
20Coot0.9 EL (ccp4)model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 294820
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13877 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initial local fitting was done chain by chain using Chimera. The model was then refine using coot and phenix.
Atomic model buildingPDB-ID: 7K00

7k00


Accession code: 7K00 / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 94.15 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0064157215
ELECTRON MICROSCOPYf_angle_d0.662235261
ELECTRON MICROSCOPYf_chiral_restr0.040930012
ELECTRON MICROSCOPYf_plane_restr0.004412521
ELECTRON MICROSCOPYf_dihedral_angle_d16.755273172

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