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- EMDB-0261: E. coli 70S d2d8 stapled ribosome -

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Basic information

Entry
Database: EMDB / ID: 0261
TitleE. coli 70S d2d8 stapled ribosome
Map datamap
SampleE. coli 70S d2d8 stapled ribosome:
(nucleic-acidNucleic acid) x 2 / (50S ribosomal protein ...) x 31 / (30S ribosomal protein ...) x 20 / (ligand) x 3
Function / homologyRibosomal protein S14, bacterial/plastid / Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L36 superfamily ...Ribosomal protein S14, bacterial/plastid / Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L31 type A / Ribosomal protein S20 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein S11 superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein S21 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S10 domain / Ribosomal protein L28/L24 / Ribosomal protein S7p/S5e / Ribosomal protein L9, N-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, C-terminal / Ribosomal protein L16, conserved site / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L10 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S12/S23 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L3, conserved site / KH domain / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein S7 signature. / Ribosomal protein L23 signature. / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L9, C-terminal domain / Ribosomal protein S18 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal L32p protein family
Function and homology information
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 2.96 Å resolution
AuthorsSchmied WH / Tnimov Z / Uttamapinant C / Rae CD / Fried SD / Chin JW
CitationJournal: Nature / Year: 2018
Title: Controlling orthogonal ribosome subunit interactions enables evolution of new function.
Authors: Wolfgang H Schmied / Zakir Tnimov / Chayasith Uttamapinant / Christopher D Rae / Stephen D Fried / Jason W Chin
Validation ReportPDB-ID: 6hrm

SummaryFull reportAbout validation report
DateDeposition: Sep 27, 2018 / Header (metadata) release: Dec 19, 2018 / Map release: Dec 19, 2018 / Last update: Jan 2, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6hrm
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0261.map.gz (map file in CCP4 format, 202613 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
370 pix
1.06 Å/pix.
= 392.2 Å
370 pix
1.06 Å/pix.
= 392.2 Å
370 pix
1.06 Å/pix.
= 392.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.11 (by author), 0.11 (movie #1):
Minimum - Maximum-0.6023513 - 0.87504876
Average (Standard dev.)0.0009955532 (0.02841988)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions370370370
Origin0.00.00.0
Limit369.0369.0369.0
Spacing370370370
CellA=B=C: 392.19998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z392.200392.200392.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS370370370
D min/max/mean-0.6020.8750.001

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Supplemental data

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Sample components

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Entire E. coli 70S d2d8 stapled ribosome

EntireName: E. coli 70S d2d8 stapled ribosome / Number of components: 57

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Component #1: protein, E. coli 70S d2d8 stapled ribosome

ProteinName: E. coli 70S d2d8 stapled ribosome / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #2: nucleic-acid, stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 1...

Nucleic-acidName: stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU AAUACCGCAU AACGUCGCAA GACCAAAGAG GGGGACCUUC GGGCCUCUUG CCAUCGGAUG UGCCCAGAUG GGAUUAGCUA GUAGGUGGGG UAACGGCUCA CCUAGGCGAC GAUCCCUAGC UGGUCUGAGA GGAUGACCAG CCACACUGGA ACUGAGACAC GGUCCAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGC ACAAUGGGCG CAAGCCUGAU GCAGCCAUGC CGCGUGUAUG AAGAAGGCCU UCGGGUUGUA AAGUACUUUC AGCGGGGAGG AAGGGAGUAA AGUUAAUACC UUUGCUCAUU GACGUUACCC GCAGAAGAAG CACCGGCUAA CUCCG(PSU)GCCA GCAGCC(7MG)CGG UAAUACGGAG GGUGCAAGCG UUAAUCGGAA UUACUGGGCG UAAAGCGCAC GCAGGCGGUU UGUUAAGUCA GAUGUGAAAU CCCCGGGCUC AACCUGGGAA CUGCAUCUGA UACUGGCAAG CUUGAGUCUC GUAGAGGGGG GUAGAAUUCC AGGUGUAGCG GUGAAAUGCG UAGAGAUCUG GAGGAAUACC GGUGGCGAAG GCGGCCCCCU GGACGAAGAC UGACGCUCAG GUGCGAAAGC GUGGGGAGCA AACAGGAUUA GAUACCCUGG UAGUCCACGC CGUAAACGAU GUCGACUUGG AGGUUGUGCC CUUGAGGCGU GGCUUCCGGA GCUAACGCGU UAAGUCGACC GCCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU UCGAU(2MG)(5MC)AAC GCGAAGAACC UUACCUGGUC UUGACAUCCA CGGAAGUUUU CAGAGAUGAG AAUGUGCCUU CGGGAACCGU GAGACAGGUG CUGCAUGGCU GUCGUCAGCU CGUGUUGUGA AAUGUUGGGU UAAGUCCCGC AACGAGCGCA ACCCUUAUCC UUUGUUGCCA GCGGUCCGGC CGGGAACUCA AAGGAGACUG CCAGUGAUAA ACUGGAGGAA GGUGGGGAUG ACGUCAAGUC AUCAUG(2MG)CCC UUACGACCAG GGCUACACAC GUGCUACAAU GGCGCAUACA AAGAGAAGCG ACCUCGCGAG AGCAAGCGGA CCUCAUAAAG UGCGUCGUAG UCCGGAUUGG AGUCUGCAAC UCGACUCCAU GAAGUCGGAA UCGCUAGUAA UCGUGGAUCA GAAUGCCACG GUGAAUACGU UCCCGGGCCU UGUACACACC G(4OC)CCGU(5MC)ACA CCAUGGGAGU GGGUUGCAAA AGAAGUAGGU AGCUUAACCG GUCAACAGCC GUUUGAGCUA ACCGGUACUA AUGAACCGUG AGGCUUAACC UUGAGAGGUU AAGCGACUAA GCGUACACGG UGGAUGCCCU GGCAGUCAGA GGCGAUGAAG GACGUGCUAA UCUGCGAUAA GCGUCGGUAA GGUGAUAUGA ACCGUUAUAA CCGGCGAUUU CCGAAUGGGG AAACCCAGUG UGUUUCGACA CACUAUCAUU AACUGAAUCC AUAGGUUAAU GAGGCGAACC GGGGGAACUG AAACAUCUAA GUACCCCGAG GAAAAGAAAU CAACCGAGAU UCCCCCAGUA GCGGCGAGCG AACGGGGAGC AGCCCAGAGC CUGAAUCAGU GUGUGUGUUA GUGGAAGCGU CUGGAAAGGC GCGCGAUACA GGGUGACAGC CCCGUACACA AAAAUGCACA UGCUGUGAGC UCGAUGAGUA GGGCGGGACA CGUGGUAUCC UGUCUGAAUA UGGGGGGACC AUCCUCCAAG GCUAAAUACU CCUGACUGAC CGAUAGUGAA CCAGUACCGU GAGGGAAAGG CGAAAAGAAC CCCGGCGAGG GGAGUGAAAA AGAACCUGAA ACCGUGUACG UACAAGCAGU GGGAGCACGC UUAGGCGUGU GACUGCGUAC CUUUUGUAUA AUGGGUCAGC GACUUAUAUU CUGUAGCAAG GUUAACCGAA UAGGGGAGCC GAAGGGAAAC CGAGUCUUAA CUGGGCGUUA AGUUGCAGGG UAUAGACCCG AAACCCGGUG AUCUAGCCAU GGGCAGGUUG AAGGUUGGGU AACACUAACU GGAGGACCGA ACCGACUAAU (1MG)(PSU)(5MU)GAAAAAU UAGCGGAUGA CUUGUGGCUG GGGGUGAAAG GCCAAUCAAA CCGGGAGAUA GCUGGUUCUC CCCGAAAGCU AUUUAGGUAG CGCCUCGUGA AUUCAUCUCC GGGGGUAGAG CACUGUUUCG GCAAGGGGGU CAUCCCGACU UACCAACCCG AUGCAAACUG CGAAUACCGG AGAAUGUUAU CACGGGAGAC ACACGGCGGG (PSU)GCUAACGUC CGUCGUGAAG AGGGAAACAA CCCAGACCGC CAGCUAAGGU CCCAAAGUCA UGGUUAAGUG GGAAACGAUG UGGGAAGGCC CAGACAGCCA GGAUGUUGGC UUAGAAGCAG CCAUCAUUUA AAGAAAGCGU AAUAGCUCAC UGGUCGAGUC GGCCUGCGCG GAAGAUGUAA CGGGGCUAAA CCAUGCACCG AAGCUGCGGC AGCGACGCUU AUGCGUUGUU GGGUAGGGGA GCGUUCUGUA AGCCUGCGAA GGUGUGCUGU GAGGCAUGCU GGAGGUAUCA GAAGUGCGAA UGCUGACAUA AGUAACGAUA AAGCGGGUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUAA GGCGAGGCCG AAAGGCGUAG UCGAUGGGAA ACAGGUUAAU AUUCCUGUAC UUGGUGUUAC UGCGAAGGGG GGACGGAGAA GGCUAUGUUG GCCGGGCGAC GGUUGUCCCG GUUUAAGCGU GUAGGCUGGU UUUCCAGGCA AAUCCGGAAA AUCAAGGCUG AGGCGUGAUG ACGAGGCACU ACGGUGCUGA AGCAACAAAU GCCCUGCUUC CAGGAAAAGC CUCUAAGCAU CAGGUAACAU CAAAUCGUAC CCCAAACCGA CAC(6MZ)GGUGGU CAGGUAGAGA AUACCAAGGC GCUUGAGAGA ACUCGGGUGA AGGAACUAGG CAAAAUGGUG CCGUAACUUC GGGAGAAGGC ACGCUGAUAU GUAGGUGAGG UCCCUCGCGG AUGGAGCUGA AAUCAGUCGA AGAUACCAGC UGGCUGCAAC UGUUUAUUAA AAACACAGCA CUGUGCAAAC ACGAAAGUGG ACGUAUACGG UGUGACGCCU (2MG)CCCGGUGCC GGAAGGUUAA UUGAUGGGGU UAGCGCAAGC GAAGCUCUUG AUCGAAGCCC CGGUAAACGG CGGCCG(PSU)AAC (3TD)A(PSU)AACGGUC CUAAGGUAGC GAAA(5MU)UCCUU GUCGGGUAAG UUCCGAC(5MC)UG CACGAAUGGC GUAAUGAUGG CCAGGCUGUC UCCACCCGAG ACUCAGUGAA AUUGAACUCG CUGUG(6MZ)AGAU GCAGUGUACC CGCGGCAAGA CGGAAAGACC CCGU(G7M)AACCU UUACUAUAGC UUGACACUGA ACAUUGAGCC UUGAUGUGUA GGAUAGGUGG GAGGCUUUGA AGUGUGGACG CCAGUCUGCA UGGAGCCGAC CUUGAAAUAC CACCCUUUAA UGUUUGAUGU UCUAACGUUG ACCCGUAAUC CGGGUUGCGG ACAGUGUCUG GUGGGUAGUU UGACUG(OMG)GGC GGUCUCCUCC UAAAGAGUAA CGGAGGAGCA CGAAGGUUGG CUAAUCCUGG UCGGACAUCA GGAGGUUAGU GCAAUGGCAU AAGCCAGCUU GACUGCGAGC GUGACGGCGC GAGCAGGUGC GAAAGCAGGU CAUAGUGAUC CGGUGGUUCU GAAUGGAAGG GCCAUCGCUC AACGGAUAAA AGGUACUCCG (2MG)GGAUAACAG GC(PSU)GAUACCG CCCAAGAGUU CAUAUCGACG GCGGUGUUUG GCA(OMC)CUCG(2MA)(PSU) GUCGGCUCAU CACAUCCUGG GGCUGAAGUA GGUCCCAAGG GUAUGGC(OMU)GU UCGCCAUUUA AAGUGGUACG CGAGC(PSU)GGGU UUAGAACGUC GUGAGACAGU (PSU)CGGUCCCUA UCUGCCGUGG GCGCUGGAGA ACUGAGGGGG GCUGCUCCUA GUACGAGAGG ACCGGAGUGG ACGCAUCACU GGUGUUCGGG UUGUCAUGCC AAUGGCACUG CCCGGUAGCU AAAUGCGGAA GAGAUAAGUG CUGAAAGCAU CUAAGCACGA AACUUGCCCC GAGAUGAGUU CUCCCUGACC CUUUAAGGGU CCUGAAGGAA CGUUGAAGAC GACGACGUUG AUAGGCCGGG UGUGUAAACG GACAUGGUUG GAGGGCGCUU ACCACUUUGU GAUUCAUGAC UGGGGUGAAG UCG(UR3)AACAAG GUAACCGUAG G(2MG)G(MA6)(MA6)CCUGC GGUUGGAUCA CCUCCUUA
MassTheoretical: 1.445685 MDa
SourceSpecies: Escherichia coli (E. coli)

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Component #3: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCUC CCCAUGCGAG AGUAGGGAAC UGCCAGGCAU
MassTheoretical: 38.79009 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #4: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.663244 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #5: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #6: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #7: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.073234 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #8: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.672418 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #9: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #10: protein, 50S ribosomal protein L10

ProteinName: 50S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.981147 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #11: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.090395 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #12: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #13: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.565067 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #14: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.008471 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #15: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #16: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.592823 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #17: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.663471 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #18: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.028082 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #19: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.396828 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #20: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #21: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #22: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.66156 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #23: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.208054 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #24: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #25: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.275498 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #26: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.896354 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #27: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.155267 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #28: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.423625 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #29: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.516693 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #30: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.332249 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #31: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.057179 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #32: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #33: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.181835 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #34: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #35: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.072867 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #36: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.248994 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #37: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.383002 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #38: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.475037 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #39: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.125993 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #40: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.861523 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #41: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.015361 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #42: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.554882 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #43: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.254041 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #44: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.4872 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #45: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.683053 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #46: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.868091 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #47: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.475364 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #48: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.159621 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #49: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #50: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.263946 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #51: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.734896 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #52: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.421018 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #53: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.577268 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #54: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.392844 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #55: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 436 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #56: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #57: ligand, water

LigandName: water / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

-
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: 27 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 94371
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 5MDZ
Output model

+
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