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- EMDB-45185: Cutibacterium acnes 50S ribosomal subunit with Clindamycin bound -

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Basic information

Entry
Database: EMDB / ID: EMD-45185
TitleCutibacterium acnes 50S ribosomal subunit with Clindamycin bound
Map dataunsharpened map, flipped
Sample
  • Complex: 50S subunit with Clindamycin bound
    • Protein or peptide: x 29 types
    • RNA: x 2 types
  • Ligand: x 4 types
Keywordsribosome / clindamycin / acne / ANTIBIOTIC
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / : / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2, conserved site / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L5 domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 ...Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL17 / 50S ribosomal protein bL37 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL21
Similarity search - Component
Biological speciesCutibacterium acnes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsLomakin IB / Devarkar SC / Bunick CG
Funding support Canada, 1 items
OrganizationGrant numberCountry
Ortho Dermatologics Canada
CitationJournal: J Invest Dermatol / Year: 2024
Title: Mechanistic Basis for the Translation Inhibition of Cutibacterium acnes by Clindamycin.
Authors: Ivan B Lomakin / Swapnil C Devarkar / Ayman Grada / Christopher G Bunick /
Abstract: Inflammation and the Gram-positive anaerobic bacterium Cutibacterium acnes, which is implicated in acne pathogenesis and pilosebaceous-unit inflammation, are the main targets of antibiotic-based ...Inflammation and the Gram-positive anaerobic bacterium Cutibacterium acnes, which is implicated in acne pathogenesis and pilosebaceous-unit inflammation, are the main targets of antibiotic-based therapy against acne vulgaris (acne). The most widely used antibiotics in acne therapy are tetracyclines, macrolides, and lincosamides. Unfortunately, C. acnes bacteria over the past several decades have demonstrated increased resistance to these antibiotics, particularly to clindamycin. The precise knowledge of how antibiotics interact with their clinical target is needed to overcome this problem. Toward this goal, we determined the structure of clindamycin in complex with the ribosome of C. acnes at 2.53 Å resolution using cryogenic electron microscopy. The galactose sugar moiety of clindamycin interacts with nucleotides of the 23S ribosomal RNA directly or through a conserved network of water-mediated interactions. Its propyl pyrrolidinyl group interacts with the 23S ribosomal RNA through van der Waals forces. Clindamycin binding to the C. acnes ribosome interferes with both: proper orientation of the aminoacyl group of the A-site bound transfer RNA that is needed for peptide bond formation and with the extension of the nascent peptide. Our data are important for advancing the understanding of antibiotic resistance and development of narrow-spectrum antibacterial drugs, which is an urgent need for contemporary antibiotic stewardship.
History
DepositionJun 4, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45185.png

Downloads & links

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Map

FileDownload / File: emd_45185.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map, flipped
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 400 pix.
= 347.2 Å		0.87 Å/pix.
x 400 pix.
= 347.2 Å		0.87 Å/pix.
x 400 pix.
= 347.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.868 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.35139596 - 1.1093585
Average (Standard dev.)0.00025311203 (±0.050954327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 347.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45185_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_45185_half_map_2.map
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Sample components

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Entire : 50S subunit with Clindamycin bound

EntireName: 50S subunit with Clindamycin bound
Components
  • Complex: 50S subunit with Clindamycin bound
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: Large ribosomal subunit protein bL17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: Large ribosomal subunit protein bL21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: Large ribosomal subunit protein bL35
    • Protein or peptide: 50S ribosomal protein L31
    • RNA: 23S rRNA
    • RNA: 5S rRNA
    • Protein or peptide: 50S ribosomal protein bL37
    • Protein or peptide: 50S ribosomal protein L36
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: CLINDAMYCIN
  • Ligand: water

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Supramolecule #1: 50S subunit with Clindamycin bound

SupramoleculeName: 50S subunit with Clindamycin bound / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#31
Source (natural)Organism: Cutibacterium acnes (bacteria)

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Macromolecule #1: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 30.309863 KDa
SequenceString: MGIRKYKPTT PGRRGSSVSD FVELTRSTPE KSLLVAKPKT GGRNNTGRIT TRHIGGGHKQ AYRIIDFKRY DKDGVPAKVA HIEYDPNRT ARIALLHYAD GEKRYIIAPD GVGQGTVVVS GPEADIKPGN NLPLRNIPVG TTVHAVELRP GGGAKMGRSA G ASVQLVAR ...String:
MGIRKYKPTT PGRRGSSVSD FVELTRSTPE KSLLVAKPKT GGRNNTGRIT TRHIGGGHKQ AYRIIDFKRY DKDGVPAKVA HIEYDPNRT ARIALLHYAD GEKRYIIAPD GVGQGTVVVS GPEADIKPGN NLPLRNIPVG TTVHAVELRP GGGAKMGRSA G ASVQLVAR EGKYATVRLP SGEMRMVDIR CRATIGEVGN AEQININWGK AGRNRWKGIR PTVRGVVMNP IDHPHGGGEG RT SGGRHPV SPWGKPEGRT RNKKKASSRL IVRRRKSGKK R

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #2: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 23.553053 KDa
SequenceString: MTNERTVKGV LGTKLGMTQL WDEHNRLVPV TVIQAGPCVV TQVRTPETDG YSAVQLGYGA VKAKNVTKPE AGHFEKAGVT PRRHLVELR TADASEYTLG QEIAADVFSE SDFVDVTGTS KGKGTAGVMK RHGFGGLRAT HGVHRKHRSP GSIGGCSTPG K VIKGLRMA ...String:
MTNERTVKGV LGTKLGMTQL WDEHNRLVPV TVIQAGPCVV TQVRTPETDG YSAVQLGYGA VKAKNVTKPE AGHFEKAGVT PRRHLVELR TADASEYTLG QEIAADVFSE SDFVDVTGTS KGKGTAGVMK RHGFGGLRAT HGVHRKHRSP GSIGGCSTPG K VIKGLRMA GRMGVERVTV QNLQVHSVDA ERGIMLVRGA VPGPKGSLLV VRSAAKKAAK NGDAA

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #3: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 32.34217 KDa
SequenceString: MNETKTIDVL DVKGKKAGSA ELPGDLFDVN TNIPLIHQVV VAQLAAARQG THATKTRGQV SGGGKKPWRQ KGTGRARQGS TRAPQWVGG GTVHGPQPRS YAQRTPKKMV GAALRGALSD MARDNRIFVV TSLVDGDKPS TKQAKAVLSG LAELRKVLVV L DRSDEIDW ...String:
MNETKTIDVL DVKGKKAGSA ELPGDLFDVN TNIPLIHQVV VAQLAAARQG THATKTRGQV SGGGKKPWRQ KGTGRARQGS TRAPQWVGG GTVHGPQPRS YAQRTPKKMV GAALRGALSD MARDNRIFVV TSLVDGDKPS TKQAKAVLSG LAELRKVLVV L DRSDEIDW LSVRNLSEVH VLAADQLNTY DVVNARTIVF SQAGLDAFVG ARSANTQALS AEPEVPETNV ADQHPYGEDS FR GDNPPAG FDIKGNEDSM KFHEPSSPWY GRTIAEVWFR SAAAAEAAGF VNAVKSDSEK EDAK

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #4: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 23.901756 KDa
SequenceString: MSTDAIAHEM PRLKKQYREQ IRAAMQEEFG YRNPMLIPGL EKIVVNMGVG DAAHDSKVMD GAIRDITAIT GQKPQVTKAR KSIAQFKLR EGQPIGCHVT LRGDRMWEFA DRLLTLALPR IRDFRGLNSN QFDGKGNYTF GLSEQVMFLE IDQDKIDRIR G MDITFVTT ...String:
MSTDAIAHEM PRLKKQYREQ IRAAMQEEFG YRNPMLIPGL EKIVVNMGVG DAAHDSKVMD GAIRDITAIT GQKPQVTKAR KSIAQFKLR EGQPIGCHVT LRGDRMWEFA DRLLTLALPR IRDFRGLNSN QFDGKGNYTF GLSEQVMFLE IDQDKIDRIR G MDITFVTT AQTNEEGKAL LKHLGFPFKA KDDPKKAKTK RGPAYYAKKK KK

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #5: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 19.868811 KDa
SequenceString:
MSRIGRLPIA VPSGVEVKLD GQYVEVKGPK GTLNFTVREP ITVSKNDEGA ILVERPDDER ENRSLHGLTR TLINNMVIGV TEGYEKKLE IQGVGYRVLS KGPKQLEFNL GFSHPVIVDA PEGITFAVEN PTKFSVQGID KQVVGETAAN IRKIRKPEPY K GKGVRYEG ENVRRKVGKA GK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #6: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 16.325824 KDa
SequenceString:
MTTYSPKAGE VQRKWYVIDA EDIVLGRLAT TAANLLRGKH KPQYAPHIDT GDFVVVVNAS KIALTGKKAT DSLRYDHSGR PGGLRVTSI GEMLAKNPRR AVERAVWGMM PKNKLSRQQL KKLKVYGGPE HPHAAQNPQP YEITQIAQ

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #7: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.503871 KDa
SequenceString:
MIQQETRLKV ADNTGAKELL CIRVLGGSKR RYAYLGDTIV CTVKDAIPGG NVKKGEVVKA VVVRTVKSHR RPDGSYIKFD ENAAVLLKG DGEPRGTRIF GPIARELREK KFMRIVSLAP EVI

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #8: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 15.542903 KDa
SequenceString:
MAIELHDLKP APGAHKAKTR VGRGEGSKGK TAGRGTKGTG ARKNVPEFFA GGQMPIHMQA PKLGGFHNPF RTEYQVVNLD KVEALFPKG GKITVDDLVS VGAVRDNELV KVLGTGELTV KVDLVVDAWS KSAQEKIEKA GGSVTKR

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #9: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 15.700248 KDa
SequenceString:
MLIPRRVKYR KQHHPKRTGA AKGGTQLAFG DYGIQATEGG YLTNRQIEAA RIAMTRYIKR GGKVWINVYP DRPMTKHPAE SRMGSGKGT PEWWIANIKP GRVLFELSGV PEDVAREAMR LAIHKLPMKA RFISREGGDN

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #10: Large ribosomal subunit protein bL17

MacromoleculeName: Large ribosomal subunit protein bL17 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 20.058641 KDa
SequenceString:
MPKPTKGPRL GGSPAHERII LRNLASQLFE HGRVVTTVTK AKRVRPLAEK LINRAKTDTV ANRRFVNRTI TDRGIVHILF TEIGPRMEG RDGGYTRVTR IGIRKGDNAP MAVIEVISDK VAPKAPASAA DAKAQINTAT EAKDAEPEAG DAAVEHNAPA E DAAAQAPV ADEQEAAEAD EKAEEKPEA

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #11: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.727841 KDa
SequenceString:
MASTLTVRKS LSDRAKARAR RQARGRKKIF GTVERPRMVV TRSSKHVFVQ VIDDVAGNTL VSASTMEAEL REMSGDKTAK AARVGTIIG ERAKAAGITK VVFDKAGNQY HGRIAALADA AREAGLDF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #12: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.106117 KDa
SequenceString:
MSNIIDEIDK ASMRDDIPEF RPGDSVKVHV KVVEGSRTRV QVFSGIVISR TGGGVQESFT VRKLSFGTGV ERTFPLHSPI IDKIEVDRH GAVRRAKLYY LRGRRGKAAK IKERGSAR

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #13: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.988012 KDa
SequenceString:
MARVKRSVNA KKKRREVLDQ ASGYRGQRSR LYRKAKEQTL HSATYSFRDR RAKKGDFRSL WIQRINAASR AQGMTYNRFI NGLKNAGVE VDRKMLAELA VSDINAFNSL VEVAKASQPQ NAAA

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #14: Large ribosomal subunit protein bL21

MacromoleculeName: Large ribosomal subunit protein bL21 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 11.087788 KDa
SequenceString:
MYAIVRSGGR QHKVAVGDVV EIDKVADEAG SSIELTPLLV VDGESVTSDK DALGKVKVTA EVLGETKGPK IRILKYKNKT GYKKRQGHR QKYTQVKVTG IEG

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #15: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 16.729471 KDa
SequenceString:
MSKTERPSRR AALLGDRPGS YAIARHVRMS ASKCRRVINL VRGMDAVDAV TMLKFQPQAA AEPIRKVIAS AMANAEQTEG LRADDLYIS QAFVDEGITM RRIRPRAKGS ASRILKRSAH ITVVVEPKEA RQARKKAKSG RPAAAAKSET EKGA

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #16: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 11.34922 KDa
SequenceString:
MSELKIRDPR DIILAPVVSE KSYGLLDQNT YTFVVKPTAN KTEIKIAIEQ IFGVKVTSVN TMNRKGKVRR TRTGVGKRPD TKRAIVTVA EGDRIDIFTG PVA

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #17: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 17 / Details: loop 49-62 is not modeled, no EM density for it / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.514626 KDa
SequenceString:
MKSLKIKKGD RVKVIAGNDK GAIGEVLSVD PARERVVVEG VNIRKHHRRD MPTPQGGTTK GGIISSEAPI HVSNVQLVTK IDGKDVVTR VGYRRVDVTK RRPDGSEYAA QRSVRYLKKE EAK

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #18: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 22.349113 KDa
SequenceString: MADIIHLKAE QRTEFGKGAA RRIRRDDKVP AVMYGHDHDP IHVTLDGHAT LLALRTENPL LSIEIEGQKP MLALPKDVQR DVLKGFVRH VDLLTVRRGE KVDVNVALRI TGESAPGTIA MTEFNEIEVQ ADLLNIPEVI EIDVTGLEAG TTIYLGDLKL P EGTSLLGD ...String:
MADIIHLKAE QRTEFGKGAA RRIRRDDKVP AVMYGHDHDP IHVTLDGHAT LLALRTENPL LSIEIEGQKP MLALPKDVQR DVLKGFVRH VDLLTVRRGE KVDVNVALRI TGESAPGTIA MTEFNEIEVQ ADLLNIPEVI EIDVTGLEAG TTIYLGDLKL P EGTSLLGD AEDVAATVAF PETEPVEDEE SAGEDAQGES EEKAAKE

UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #19: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 9.540655 KDa
SequenceString:
MAHKKGASSS RNGRDSNAQR LGVKRFGGQL VNAGEIIVRQ RGTHFHPGDG VGRGGDDTLF ALRDGNVEFG TRRGRRVVNV TPVEAPVEA

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #20: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 6.953212 KDa
SequenceString:
MAAVCDICAK RPGFGHNVPW SKKKTNRRWS PNIQRVRVVE NGTHKRMNVC TSCLKAGRVS R

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #21: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 8.899072 KDa
SequenceString:
MPKLSAAELR QLSGEELRNK VRELKEELFG LRFQSATGQL ENTARLREVR KDIARVYTVL QERNLNIVDD PDSTKEA

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #22: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 6.932171 KDa
SequenceString:
MSKLKITQIK SGIATKPNHR ETLRSLGLKR IGDTVIKEDR PEFRGMVRTV RHLVTMEEVD

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #23: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 6.991128 KDa
SequenceString:
MAVPKRKMSR SNTRHRRSQW KTVATKLVTC ANPACGEKHL PHTACPSCGG YGPRGDRRQV VEA

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #24: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 6.725948 KDa
SequenceString:
MAKKSGDVRP KITLACTECK ERNYITKKNR RNNPDRMEMA KFCPRCRKHT AHRETR

UniProtKB: Large ribosomal subunit protein bL33

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Macromolecule #25: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 5.185076 KDa
SequenceString:
MKRTFQPSNR RRARNHGFRS RMSTRAGRSI LAARRRKGRV NLSA

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #26: Large ribosomal subunit protein bL35

MacromoleculeName: Large ribosomal subunit protein bL35 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 7.457868 KDa
SequenceString:
MPKMKSHSGT KKRFKVTGSG KVTARKAGKR HLNEHKSSRV TRRLTGETVL SKGEAAKVKK LLAGHPGR

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #27: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 7.731771 KDa
SequenceString:
MKQGIHPDYR ETTVVCTCGN TFTTRSTSQS GTLNADVCSK CHPFYTGKQK ILDAGGRVAR FERRYGKKN

UniProtKB: Large ribosomal subunit protein bL31

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Macromolecule #30: 50S ribosomal protein bL37

MacromoleculeName: 50S ribosomal protein bL37 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 2.744284 KDa
SequenceString:
MGKTGRKRRA RRKKGANHGK RPNA

UniProtKB: 50S ribosomal protein bL37

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Macromolecule #31: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 4.386379 KDa
SequenceString:
MKVQPSVKKI CDKCKVIRRH GRVMVICDNP RHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #28: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 28 / Number of copies: 1
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 1.002554625 MDa
SequenceString: GCAAAGUUGU GUAGUGCGAU CGGUGGAUGC CUUGGCACCA AGAGCCGAUG AAGGACGUUG UGACCUGCGA UAAGCCCUGG GGAGUUGGU GAGCGAGCUG UGAUCCGGGG GUGUCCGAAU GGGGAAACCU GGAAUGUCCG GAGUAGUGUC CGGUGGCCCU G CCCUGAAU ...String:
GCAAAGUUGU GUAGUGCGAU CGGUGGAUGC CUUGGCACCA AGAGCCGAUG AAGGACGUUG UGACCUGCGA UAAGCCCUGG GGAGUUGGU GAGCGAGCUG UGAUCCGGGG GUGUCCGAAU GGGGAAACCU GGAAUGUCCG GAGUAGUGUC CGGUGGCCCU G CCCUGAAU GUAUAGGGGU GUGGGUGGUA ACGCGGGGAA GUGAAACAUC UUAGUACCCG UAGGAAGAGA AAACAAGUGU GA UUCCGUG AGUAGUGGCG AGCGAAAGCG GAGGAGGCUA AACCGUGUGU GUGUUCAAGC CGGCAGGUGU UGCAUGUGCG GGG UUGUGG GGGCCUUGUG GUUCUGCUGC CGCAGGAUUG GCCAGUGAGA AAUGUUGCGU GAAGGUGAAG CGUCUGGGAA GGCG UACCG GAGUGGGUGA GAGUCCUGUA ACUGUAAGCG UGGCACUGGU GUGGGGUUGC CCCGAGUAGC GUGGGACUCG UGGAA UUUC GCGUGAAUCU GGCGGGACCA CCCGUCAAGC CUAAAUACUC CUUGGUGACC GAUAGUGGAU GAGUACCGUG AGGGAA GGG UGAAAAGUAC CCCGGGAGGG GAGUGAAAGA GUUCCUGAAA CCGGUCGCAU GCAAGCCGUC AGAGCCUGUG UGGUGAU GG CGUGCCUUUU GAAGAAUGAG CCUGCGAGUU AGUGAUGCGU GGCGAGGUUA ACCCGUGGUG GGGGAGUCGU AGCGAAAG C GAGUCCGAUA AGGGCGUGAG UCGCGUGUUC UAGACCCGAA GCGGUGUGAU CUAUCCAUGG CCAGGAUGAA GCGUCGGUA AGACGUCGUG GAGGUCCGAA CCCACUUCAG UUGAAAAUGG AGGGGAUGAG UUGUGGAUAG GGGUGAAAGG CCAAUCAAAC ACCGUGAUA GCUGGUUCUC CCCGAAAUGC AUUUAGGUGC AGCGUUGCGU GGUUCUUGUU GGAGGUAGAG CACUGGAUGG U CUAGGGGG CUUAUCGGCU UACCGAAAUC AGCCAAACUC CGAAUGCUGG CAAGUGUAGC GUGGCAGUGA GACGGCGGG (PSU)GAUAAGCUU CGUCGUCGAG AGGGAAACAG CCCAGAUCAU CAGCUAAGGC CCCUAAGUGG UGACUCAGUG GGAAAG GAU GUGGAGUUGC GUAGACAACC AGGAGGUUGG CUUGGAAGCA GCCAUCCUUG AAAGAGUGCG UAAUAGCUCA CUGGUCA AG UGAUUCCGCG CCGAUAAUGU AGCGGGGCUU AAGUUAUCCG CCGAAGCUGU GGCAACCUGU GUGGUUGGGU AGGGGAGC G UCGUGUCAGU GGUGAAGCUG CCGGGUGACU GUGUGGUGGA GUUGAUGCGA GUGAGAAUGC AGGCAUGAGU AGCGUGUGA CGGGUGGGAA UCCCGUCCGC CGAUUAUCCA AGGGUUCCAG GGUCAAGUUU GUCUGCCCUG GGUGAGUCGG GUCCUAAGGC GAGGCCGAC AGGCGUAGUC GAUGGGUAAC CAGUUGAUAU UCUGGUACCG GCUUGUCACC GUCCGUGUCG AGGUGUGUGA U GCUAAGCA UGUGAGCUUG UCUUGGGAGU GUUUUUGAUG CUUCUGGGGU GGGUGAGUGU GUGAACCGAU CAUGUAGUAG GC AAGCUGC GGAGGGACGC AGUGAGGUAG CUCAUCCCCG GUGAUGGUUG UCCGGGGCUA AGUGUGUGGA CUGUCUGGUA GGU AAAUCC GCUGGGCGUG AAGGUUGAGG CAUGAUGGGG AGCCCAUGGU UGUGGGUGAG UGAGUGAUCC UGUACUGUCG AGAA AAGCU UCGUGAGCGA GGUGGCGGGU CCGCCCGUAC CCUAAACCGA CACUGGUGGA UAGGUAGAGU AUACCGAGGC GAUCG AGUG AAUCGUGGUG AAGGAACUCG GCAAAAUGCC CCCGUAACUU UGGGAUAAGG GGGACCUGAG CUGUCGUGCA CCCGUG CGG UGUGGUGGCG GUGAGGGGCG CAGAGUCCAG GGGGAAACGA CUGUUUACCA AAAACACAGG UCCGUGCGAA GUCGUAA GA CGAUGUAUAC GGACUGACUC CU(2MG)CCCGGUG CUGGAAGGUU AAGGGGAACU GUGAGUGUAU GCGUAGCGGU GAAC UUAAG CCCCAGUAAA CGGCGGUGG(PSU) AAC(3TD)A(PSU)AACC AUCCUAAGGU AGCGAAA(5MU)UC CUUGUCGGG UAAGUUCCGA C(5MC)UGCACGAA UGGAGUAACG AUUUCCCUAC UGUCUCCACC AUGAACUCGG UGAAAUUGCA UUACGA GUA AAGAUGCUCG UUACGCGCAG CAGGACGGAA AGACCCCGGG ACCUUUACUA UAGUUUGGUA UUGGUGAUUG GGACGGU UU GUGUAGGAUA GGUGGGAGAC GUUGAUGCGG CCACGCUAGU GGUGGUGGAG UCGUUGGUGA AAUACCACUC UGAUUGUU C UGGUUAUCUC ACUGUGGACC GUGAUCCGGU UCAAGGACAG UGCCUGAUGG GUAGUUUGAC UG(OMG)GGCGGUC GCCUC CUAA AGGGUAACGG AGGCGCCCAA AGGUUCCCUC AGCCUGGUUG GUAAUCAGGU GGUGAGUGUA AGUGCACAAG GGGGCU UGA CUGUGAGACU GACAGGUCGA GCAGGGACGA AAGUCGGGAC UAGUGAUCUG ACGGUGGCUU GUGGAUGCGC CGUCACU CA ACGGAUAAAA GGUACCCCG(2MG) GGA(H2U)AACAGG C(PSU)GAUCUUGC CCGAGCGCUC AUAGCGACGG CAUGGU UUG GCA(OMC)CUCG(2MA)(PSU) GUCGGCUCGU CGCAUCCUGG GGCUGGAGUC GGUCCCAAGG GUUGGGC(OMU)GU U CGCCCAUU AAAGCGGCAC GCGAGC(PSU)GGG UUCAGAACGU CGUGAGACAG (PSU)(PSU)CGGUCCCU AUCCGCUGCG CGCGGAGGA AUCUUGAGAA GGGCUGUCUU UAGUACGAGA GGACCGAGAC GGACUGACCU CUGGUGUGCC AGUUGUUCUG C CAAGAGCA UGGCUGGUUG GCUACGUCGG GUUGUGAUAA CCGCUGAAAG CAUCUAAGCG GGAAGCACGC UUCAAGAUAA GG GUUCCCA CAGGAGUGUU CCUGGUAAGG UCCCCGAGAG AUGAUCGGGU UGAUAGGCCA GACGUGGACG CAUCGUAAGG UGU GGAGCU GACUGGUACU AAUAGACCGA GGACUUUCAU UAACA

GENBANK: GENBANK: CP012350.1

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Macromolecule #29: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 29 / Number of copies: 1
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 38.770055 KDa
SequenceString:
UUUCCGGUGG CCAUAGUGGA AGGGAAACAC CCGGUCCCAU UCCGAACCCG GUCGUUAAGC CUUCCAACGC UGAUGGUACU GCACGAGGG AUCGUGUGGG AGAGUAAGAC GCUGCCGGAA U

GENBANK: GENBANK: CP059593.1

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Macromolecule #32: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 32 / Number of copies: 247 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #33: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 33 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #34: CLINDAMYCIN

MacromoleculeName: CLINDAMYCIN / type: ligand / ID: 34 / Number of copies: 1 / Formula: CLY
Molecular weightTheoretical: 424.983 Da
Chemical component information

ChemComp-CLY:
CLINDAMYCIN / medication, antibiotic*YM

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Macromolecule #35: water

MacromoleculeName: water / type: ligand / ID: 35 / Number of copies: 156 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.8 sec. / Average electron dose: 38.58 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2674133
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 283291
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9c4g:
Cutibacterium acnes 50S ribosomal subunit with Clindamycin bound

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