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- EMDB-21907: 50S subunit of 70S Ribosome Enterococcus faecalis MultiBody refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-21907
Title50S subunit of 70S Ribosome Enterococcus faecalis MultiBody refinement
Map data
SampleEnterococcus faecalis (bacteria):
(nucleic-acidNucleic acid) x 2 / (50S ribosomal protein ...) x 25 / ligand
Function / homology
Function and homology information


large ribosomal subunit / ribosomal large subunit assembly / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L16 signature 1. / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L28 / Ribosomal protein L33, conserved site ...Ribosomal protein L16 signature 1. / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L19 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L18, bacterial-type / Ribosomal protein L27 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L20 signature. / Ribosomal protein L6, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal L28 family / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L18 / L28p-like / Ribosomal protein L20 / Ribosomal protein L16 / Ribosomal protein L30, bacterial-type / Ribosomal L32p protein family / Ribosomal L27 protein / Ribosomal protein L27 / Ribosomal protein L34 / Ribosomal protein L21 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L34 / Ribosomal protein L19 superfamily / Ribosomal protein L20 / Ribosomal protein L19 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L32p / Ribosomal protein L21-like / Ribosomal prokaryotic L21 protein / L21-like superfamily / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L13, bacterial-type / Ribosomal protein L24 / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / ribosomal L5P family C-terminus / Ribosomal protein L5, C-terminal / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L14 signature. / Ribosomal protein L14P, conserved site / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e
Similarity search - Domain/homology
50S ribosomal protein L30 / 50S ribosomal protein L13 / 50S ribosomal protein L28 / 50S ribosomal protein L33 / 50S ribosomal protein L19 / 50S ribosomal protein L32 / 50S ribosomal protein L21 / 50S ribosomal protein L27 / 50S ribosomal protein L20 / 50S ribosomal protein L35 ...50S ribosomal protein L30 / 50S ribosomal protein L13 / 50S ribosomal protein L28 / 50S ribosomal protein L33 / 50S ribosomal protein L19 / 50S ribosomal protein L32 / 50S ribosomal protein L21 / 50S ribosomal protein L27 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L17 / 50S ribosomal protein L4 / 50S ribosomal protein L24 / 50S ribosomal protein L29 / 50S ribosomal protein L6 / 50S ribosomal protein L16 / 50S ribosomal protein L36 / 50S ribosomal protein L22 / 50S ribosomal protein L15 / 50S ribosomal protein L18 / 50S ribosomal protein L5 / 50S ribosomal protein L14 / 50S ribosomal protein L23 / 50S ribosomal protein L3 / 50S ribosomal protein L34
Similarity search - Component
Biological speciesEnterococcus faecalis OG1RF (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsJogl G / Khayat R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094157 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)G12MD007603 United States
CitationJournal: Sci Rep / Year: 2020
Title: Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis.
Authors: Eileen L Murphy / Kavindra V Singh / Bryant Avila / Torsten Kleffmann / Steven T Gregory / Barbara E Murray / Kurt L Krause / Reza Khayat / Gerwald Jogl /
Abstract: Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ...Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.
History
DepositionMay 4, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wu9
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21907.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 440 pix.
= 482.68 Å
1.1 Å/pix.
x 440 pix.
= 482.68 Å
1.1 Å/pix.
x 440 pix.
= 482.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.097 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.0851723 - 0.2261516
Average (Standard dev.)-0.00046657008 (±0.009041678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 482.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0971.0971.097
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z482.680482.680482.680
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0850.226-0.000

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Supplemental data

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Sample components

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Entire Enterococcus faecalis

EntireName: Enterococcus faecalis (bacteria) / Number of components: 29

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Component #1: protein, Enterococcus faecalis

ProteinName: Enterococcus faecalis / Recombinant expression: No
MassTheoretical: 2.5 MDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #2: nucleic-acid, 23S rRNA

nucleic acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UUAAGUGAAU AAGGGCGCAC GGUGGAUGCC UUGGCACUAG GAGCCGAUGA AGGACGGGAC UAACACCGAU AUGCUUUGGG GAGCUGUAAG UAAGCUAUGA UCCAGAGAUU UCCGAAUGGG GGAACCCAAU AUCUUUUAUA GGAUAUUACU UUUCAGUGAA UACAUAGCUG ...Sequence:
UUAAGUGAAU AAGGGCGCAC GGUGGAUGCC UUGGCACUAG GAGCCGAUGA AGGACGGGAC UAACACCGAU AUGCUUUGGG GAGCUGUAAG UAAGCUAUGA UCCAGAGAUU UCCGAAUGGG GGAACCCAAU AUCUUUUAUA GGAUAUUACU UUUCAGUGAA UACAUAGCUG AUUAGAGGUA GACGCAGAGA ACUGAAACAU CUUAGUACCU GCAGGAAGAG AAAGAAAAUU CGAUUCCCUG AGUAGCGGCG AGCGAAACGG GAAGAGCCCA AACCAACAAG CUUGCUUGUU GGGGUUGUAG GACUCCGAUA UGGUAGUCUG UUAGUAUAGU UGAAGGAUUU GGAAAAUUCC GCUAAAGAGG GUGAAAGCCC CGUAGACGAA AUGCUGACAA CACCUAGGAG GAUCCUGAGU ACGGCGGAAC ACGAGAAAUU CCGUCGGAAU CCGCGGGGAC CAUCCCGCAA GGCUAAAUAC UCCCUAGUGA CCGAUAGUGA ACCAGUACCG UGAGGGAAAG GUGAAAAGCA CCCCGGAAGG GGAGUGAAAU AGAUCCUGAA ACCGUGUGCC UACAACAAGU CAAAGCUCGU UAAUGAGUGA UGGCGUGCCU UUUGUAGAAU GAACCGGCGA GUUACGAUUG CAUGCGAGGU UAAGUCGAAG AGACGGAGCC GCAGCGAAAG CGAGUCUGAA UAGGGCGAAU GAGUAUGUAG UCGUAGACCC GAAACCAUGU GAUCUACCCA UGUCCAGGUU GAAGGUGCGG UAAAACGCAC UGGAGGACCG AACCCACGUA CGUUGAAAAG UGCGGGGAUG AGGUGUGGGU AGCGGAGAAA UUCCAAACGA ACUUGGAGAU AGCUGGUUCU CUCCGAAAUA GCUUUAGGGC UAGCCUCGGA AUUGAGAAUG AUGGAGGUAG AGCACUGUUU GGACUAGGGG CCCAUCUCGG GUUACCGAAU UCAGAUAAAC UCCGAAUGCC AUUCAUUUAU AUCCGGGAGU CAGACUGCGA GUGAUAAGAU CCGUAGUCGA AAGGGAAACA GCCCAGACCA CCAGCUAAGG UCCCAAAAUA UAUGUUAAGU GGAAAAGGAU GUGGGGUUGC ACAGACAACU AGGAUGUUGG CUUAGAAGCA GCCACCAUUU AAAGAGUGCG UAAUAGCUCA CUAGUCGAGU GACCCUGCGC CGAAAAUGUA CCGGGGCUAA ACAUAUUACC GAAGCUGUGG ACUACACCAU UAGGUGUAGU GGUAGGAGAG CGUUCUAAGG GCGUUGAAGG UCGAUCGUGA GGACGGCUGG AGCGCUUAGA AGUGAGAAUG CCGGUAUGAG UAGCGAAAGA CAGGUGAGAA UCCUGUCCAC CGUAUGACUA AGGUUUCCUG GGGAAGGCUC GUCCGCCCAG GGUUAGUCGG GACCUAAGCC GAGGCCGAUA GGCGUAGGCG AUGGACAACA GGUUGAUAUU CCUGUACCAG UUGUUUUUGU UUGAGCAAUG GAGGGACGCA GUAGGCUAAG GAAUGCAUGC GAUUGGAAGU GCAUGUCCAA GCAAUGAGUC UUGAGUAGAG UUAAAUGCUU UACUCUUUAA GGACAAGUUG UGACGGGGAG CGAAAUAAUA GUAGCGAAGU UCCUGACGUC ACACUGCCAA GAAAAGCUUC UAGUGAGAAA ACAACUGCCC GUACCGUAAA CCGACACAGG UAGUCGAGGA GAGUAUCCUA AGGUGAGCGA GCGAACUCUC GUUAAGGAAC UCGGCAAAAU GACCCCGUAA CUUCGGGAGA AGGGGUGCUG ACUUCGGUCA GCCGCAGUGA AUAGGCCCAA GCGACUGUUU AUCAAAAACA CAGGUCUCUG CAAAAUCGUA AGAUGAAGUA UAGGGGCUGA CGCCUGCCCG GUGCUGGAAG GUUAAGAGGA UGGGUUAGCU UCGGCGAAGC UCAGAAUUGA AGCCCCAGUA AACGGCGGCC GUAACUAUAA CGGUCCUAAG GUAGCGAAAU UCCUUGUCGG GUAAGUUCCG ACCCGCACGA AAGGCGUAAC GAUUUGGGCA CUGUCUCAAC GAGAGACUCG GUGAAAUUUU AGUACCUGUG AAGAUGCAGG UUACCCGCGA CAGGACGGAA AGACCCCAUG GAGCUUUACU GUAGUUUGAU AUUGAGUGUU UGUACCACAU GUACAGGAUA GGUAGGAGCC GAUGAGACCG GAACGCUAGU UUCGGAGGAG GCGCUGGUGG GAUACUACCC UUGUGUUAUG AACCCUCUAA CCCGCACCAC UAAUCGUGGU GGGAGACAGU GUCAGAUGGG CAGUUUGACU GGGGCGGUCG CCUCCUAAAA GGUAACGGAG GCGCCCAAAG GUUCCCUCAG AAUGGUUGGA AAUCAUUCGA AGAGUGUAAA GGCAGAAGGG AGCUUGACUG CGAGACCUAC AAGUCGAGCA GGGACGAAAG UCGGGCUUAG UGAUCCGGUG GUUCCGCAUG GAAGGGCCAU CGCUCAACGG AUAAAAGCUA CCCUGGGGAU AACAGGCUUA UCUCCCCCAA GAGUCCACAU CGACGGGGAG GUUUGGCACC UCGAUGUCGG CUCGUCGCAU CCUGGGGCUG UAGUCGGUCC CAAGGGUUGG GCUGUUCGCC CAUUAAAGCG GCACGCGAGC UGGGUUCAGA ACGUCGUGAG ACAGUUCGGU CCCUAUCCGU CGCGGGCGUU GGAAAUUUGA GAGGAGCUGU CCUUAGUACG AGAGGACCGG GAUGGACUUA CCGCUGGUGU ACCAGUUGUU CUGCCAAGGG CAUUGCUGGG UAGCUAUGUA GGGAAGGGAU AAACGCUGAA AGCAUCUAAG UGUGAAGCCC ACCUCAAGAU GAGAUUUCCC AUUUCUUUAA GAAAGUAAGA CCCCUGAGAG AUGAUCAGGU AGAUAGGUUG GAAGUGGAAG GCUAGUGAUA GUUGGAGCGG ACCAAUACUA AUCGGUCGAG GACUUAAC
MassTheoretical: 942.67575 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #3: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGUGGUGGCG AUAGCGAGAA GGAUACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUU CUUAGCGCCG AUUGUAGUGA AGGGUUUCCC UUUGUGAGAG UAGGACGUCG CCACGC
MassTheoretical: 37.433188 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #4: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.498104 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #5: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.384504 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #6: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.863113 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #7: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.164871 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #8: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.099585 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #9: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.165275 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #10: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.602868 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #11: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.960901 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #12: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.156251 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #13: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.806634 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #14: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.113282 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #15: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.542957 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #16: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.166986 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #17: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.126077 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #18: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.297111 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #19: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.892797 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #20: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.146118 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #21: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.072187 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #22: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.211366 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #23: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.234273 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #24: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.217372 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #25: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.052027 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #26: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.373507 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #27: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.466941 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #28: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.440534 kDa
SourceSpecies: Enterococcus faecalis OG1RF (bacteria)

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Component #29: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 100 %
Details: Vol = 4 uL, BT = 4 sec, BF = 0, DT = 0, WT = 8 sec.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 335675
3D reconstructionSoftware: cryoSPARC / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Correlation Coefficient / Refinement space: REAL
Input PDB model: 5LI0, 4YBB
Overall bvalue: 177
Output model

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