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- PDB-6u48: E. coli 50S with phazolicin (PHZ) bound in exit tunnel -

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Basic information

Entry
Database: PDB / ID: 6u48
TitleE. coli 50S with phazolicin (PHZ) bound in exit tunnel
Components
  • (50S ribosomal protein ...) x 29
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • phazolicin
KeywordsRIBOSOME/INHIBITOR / ribosome / phazolicin / antimicrobial protein / RIBOSOME-INHIBITOR complex
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site ...Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11 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 L11, N-terminal / 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 protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / 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 L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / 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 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, N-terminal
Similarity search - Domain/homology
phazolicin / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / : ...phazolicin / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / : / Large ribosomal subunit protein bL36 / 50S ribosomal protein L24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL2 / 50S ribosomal protein L3 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L21 / 50S ribosomal protein L13 / 50S ribosomal protein L9 / Large ribosomal subunit protein uL29 / 50S ribosomal protein L23 / 50S ribosomal protein L11 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L18 / 50S ribosomal protein L16 / 50S ribosomal protein L19 / 50S ribosomal protein L33 / Large ribosomal subunit protein bL32 / 50S ribosomal protein L28 / 50S ribosomal protein L5
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Rhizobium sp. Pop5 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsWatson, Z.L. / Cate, J.H.D. / Polikanov, Y.S. / Severinov, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM R01-114454 United States
National Science Foundation (NSF, United States)1106400 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition.
Authors: Dmitrii Y Travin / Zoe L Watson / Mikhail Metelev / Fred R Ward / Ilya A Osterman / Irina M Khven / Nelli F Khabibullina / Marina Serebryakova / Peter Mergaert / Yury S Polikanov / Jamie H D ...Authors: Dmitrii Y Travin / Zoe L Watson / Mikhail Metelev / Fred R Ward / Ilya A Osterman / Irina M Khven / Nelli F Khabibullina / Marina Serebryakova / Peter Mergaert / Yury S Polikanov / Jamie H D Cate / Konstantin Severinov /
Abstract: Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides ...Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ) - an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants. The cryo-EM structure of the Escherichia coli 70S-PHZ complex reveals that the drug interacts with the 23S rRNA and uL4/uL22 proteins and obstructs ribosomal exit tunnel in a way that is distinct from other compounds. We show that the uL4 loop sequence determines the species-specificity of antibiotic action. PHZ expands the known diversity of LAPs and may be used in the future as biocontrol agent for agricultural needs.
History
DepositionAug 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 2.0Nov 27, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code / _pdbx_audit_support.funding_organization
Revision 2.1Apr 1, 2020Group: 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
Revision 2.2Aug 12, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
CA: 23S rRNA
CB: 5S rRNA
CC: 50S ribosomal protein uL2
CD: 50S ribosomal protein uL3
CE: 50S ribosomal protein uL4
CF: 50S ribosomal protein uL5
CG: 50S ribosomal protein uL6
CH: 50S ribosomal protein bL9
CJ: 50S ribosomal protein uL11
CK: 50S ribosomal protein uL13
CL: 50S ribosomal protein uL14
CM: 50S ribosomal protein uL15
CN: 50S ribosomal protein uL16
CO: 50S ribosomal protein bL17
CP: 50S ribosomal protein uL18
CQ: 50S ribosomal protein bL19
CR: 50S ribosomal protein bL20
CS: 50S ribosomal protein bL21
CT: 50S ribosomal protein uL22
CU: 50S ribosomal protein uL23
CV: 50S ribosomal protein uL24
CW: 50S ribosomal protein bL25
CX: 50S ribosomal protein bL27
CY: 50S ribosomal protein bL28
CZ: 50S ribosomal protein uL29
C0: 50S ribosomal protein uL30
C1: 50S ribosomal protein bL32
C2: 50S ribosomal protein bL33
C3: 50S ribosomal protein bL34
C4: 50S ribosomal protein bL35
C5: 50S ribosomal protein bL36
A: phazolicin


Theoretical massNumber of molelcules
Total (without water)1,352,66532
Polymers1,352,66532
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Mass spectrometry used to identify phazolicin
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules CACB

#1: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 941092.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38177.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1266940032

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50S ribosomal protein ... , 29 types, 29 molecules CCCDCECFCGCHCJCKCLCMCNCOCPCQCRCSCTCUCVCWCXCYCZC0C1C2C3C4C5

#3: Protein 50S ribosomal protein uL2 /


Mass: 29663.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A1X3I1Y9
#4: Protein 50S ribosomal protein uL3 /


Mass: 22291.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A1X3JBR5
#5: Protein 50S ribosomal protein uL4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9F6
#6: Protein 50S ribosomal protein uL5 /


Mass: 20073.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: V8K465
#7: Protein 50S ribosomal protein uL6 /


Mass: 18801.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A080FKA9
#8: Protein 50S ribosomal protein bL9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZI15
#9: Protein 50S ribosomal protein uL11 /


Mass: 14020.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: H4KQ36
#10: Protein 50S ribosomal protein uL13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZET0
#11: Protein 50S ribosomal protein uL14 /


Mass: 13451.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A140N3H4
#12: Protein 50S ribosomal protein uL15 /


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6
#13: Protein 50S ribosomal protein uL16 /


Mass: 15327.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: J7RVN4
#14: Protein 50S ribosomal protein bL17 /


Mass: 13721.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0A8UJP9
#15: Protein 50S ribosomal protein uL18 /


Mass: 12663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: I2X628
#16: Protein 50S ribosomal protein bL19 /


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: L2UTN8
#17: Protein 50S ribosomal protein bL20 /


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: I2RGN4
#18: Protein 50S ribosomal protein bL21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZEN7
#19: Protein 50S ribosomal protein uL22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G0
#20: Protein 50S ribosomal protein uL23 /


Mass: 10546.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: H4IXX7
#21: Protein 50S ribosomal protein uL24 /


Mass: 11078.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0G3K7Z5
#22: Protein 50S ribosomal protein bL25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7XH79
#23: Protein 50S ribosomal protein bL27 /


Mass: 8174.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A1X3JCC7
#24: Protein 50S ribosomal protein bL28 /


Mass: 8896.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: V8F9Y0
#25: Protein 50S ribosomal protein uL29 /


Mass: 7155.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D8E8E5
#26: Protein 50S ribosomal protein uL30 /


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A073UEE9
#27: Protein 50S ribosomal protein bL32 /


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: V0ZMP5
#28: Protein/peptide 50S ribosomal protein bL33 /


Mass: 5814.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: L4V2B0
#29: Protein/peptide 50S ribosomal protein bL34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MGC4
#30: Protein 50S ribosomal protein bL35 /


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: I2RJ64
#31: Protein/peptide 50S ribosomal protein bL36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0E2L017

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Protein/peptide , 1 types, 1 molecules A

#32: Protein/peptide phazolicin


Type: Peptide-like / Class: Antimicrobial / Mass: 2054.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhizobium sp. Pop5 (bacteria) / References: phazolicin

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Details

Has ligand of interestY

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1E. coli ribosome with phazolicin in exit tunnelCOMPLEXRibosomal small subunit is not modeled due to poor density in reconstructionall0MULTIPLE SOURCES
2E. coli 50SRIBOSOME#1-#311NATURAL
3PhazolicinCOMPLEX#321NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Rhizobium sp. Pop5 (bacteria)1223565
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_3051refinement
PHENIXdev_3051refinement
EM software
IDNameVersionCategory
4CTFFIND4CTF correction
7PHENIXmodel fitting
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65393 / Symmetry type: POINT
Atomic model buildingPDB-ID: 4YBB

4ybb


Accession code: 4YBB / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005299072
ELECTRON MICROSCOPYf_angle_d0.8971148734
ELECTRON MICROSCOPYf_chiral_restr0.046719056
ELECTRON MICROSCOPYf_plane_restr0.00697619
ELECTRON MICROSCOPYf_dihedral_angle_d15.875252581

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