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- EMDB-3663: RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly inte... -

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Basic information

Entry
Database: EMDB / ID: EMD-3663
TitleRsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly intermediate with uS3)
Map data
Sample30S ribosomal subunit bound by RsgA
  • nucleic-acidNucleic acid
  • (30S ribosomal protein ...) x 18
  • Small ribosomal subunit biogenesis GTPase RsgA
  • (ligand) x 3
Function / homology
Function and homology information


guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / transcription antitermination / ribosomal small subunit biogenesis ...guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / transcription antitermination / ribosomal small subunit biogenesis / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity, mRNA regulatory element binding / endodeoxyribonuclease activity / positive regulation of RNA splicing / DNA-templated transcription, termination / positive regulation of translational fidelity / maintenance of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / GDP binding / cytosolic small ribosomal subunit / regulation of translation / regulation of mRNA stability / small ribosomal subunit / negative regulation of translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / response to antibiotic / RNA binding / membrane / metal ion binding / cytosol
Ribosomal protein S19, bacterial-type / Ribosomal protein S3, C-terminal / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S14 ...Ribosomal protein S19, bacterial-type / Ribosomal protein S3, C-terminal / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S14 / K Homology domain, type 2 / Ribosomal protein S5 / Ribosomal protein S9 / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S17/S11 / RNA-binding S4 domain / K Homology domain / Ribosomal S11, conserved site / Ribosomal protein S12/S23 / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5, N-terminal / Nucleic acid-binding, OB-fold / Ribosomal protein S13-like, H2TH / RsgA GTPase domain / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Ribosomal protein S4, conserved site / Ribosome biogenesis GTPase RsgA / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / Ribosomal protein S5/S7 / Ribosomal protein S5, N-terminal, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S8 superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S20 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S14/S29 / Ribosomal protein S19, superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S11, bacterial-type / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S4/S9 / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6, conserved site / Ribosomal protein S19 conserved site
30S ribosomal protein S3 / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S9 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S4 / 30S ribosomal protein S16 / 30S ribosomal protein S20 ...30S ribosomal protein S3 / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S9 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S4 / 30S ribosomal protein S16 / 30S ribosomal protein S20 / 30S ribosomal protein S19 / 30S ribosomal protein S18 / 30S ribosomal protein S13 / 30S ribosomal protein S12 / 30S ribosomal protein S11 / 30S ribosomal protein S10 / 30S ribosomal protein S7 / 30S ribosomal protein S6 / Small ribosomal subunit biogenesis GTPase RsgA
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.16 Å
AuthorsLopez-Alonso JP / Kaminishi T / Kikuchi T / Hirata Y / Iturrioz I / Dhimole N / Schedlbauer A / Hase Y / Goto S / Kurita D ...Lopez-Alonso JP / Kaminishi T / Kikuchi T / Hirata Y / Iturrioz I / Dhimole N / Schedlbauer A / Hase Y / Goto S / Kurita D / Muto A / Zhou S / Naoe C / Mills DJ / Gil-Carton D / Takemoto C / Himeno H / Fucini P / Connell SR
CitationJournal: Nucleic Acids Res / Year: 2017
Title: RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket.
Authors: Jorge Pedro López-Alonso / Tatsuya Kaminishi / Takeshi Kikuchi / Yuya Hirata / Idoia Iturrioz / Neha Dhimole / Andreas Schedlbauer / Yoichi Hase / Simon Goto / Daisuke Kurita / Akira Muto / ...Authors: Jorge Pedro López-Alonso / Tatsuya Kaminishi / Takeshi Kikuchi / Yuya Hirata / Idoia Iturrioz / Neha Dhimole / Andreas Schedlbauer / Yoichi Hase / Simon Goto / Daisuke Kurita / Akira Muto / Shu Zhou / Chieko Naoe / Deryck J Mills / David Gil-Carton / Chie Takemoto / Hyouta Himeno / Paola Fucini / Sean R Connell /
Abstract: During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, ...During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, namely, kinetically trapped particles. Among the assembly factors, the circularly permuted GTPase, RsgA, plays a crucial role in the maturation of the 30S decoding center. Here, directed hydroxyl radical probing and single particle cryo-EM are employed to elucidate RsgA΄s mechanism of action. Our results show that RsgA destabilizes the 30S structure, including late binding r-proteins, providing a structural basis for avoiding kinetically trapped assembly intermediates. Moreover, RsgA exploits its distinct GTPase pocket and specific interactions with the 30S to coordinate GTPase activation with the maturation state of the 30S subunit. This coordination validates the architecture of the decoding center and facilitates the timely release of RsgA to control the progression of 30S biogenesis.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionApr 10, 2017-
Header (metadata) releaseMay 31, 2017-
Map releaseMay 31, 2017-
UpdateSep 13, 2017-
Current statusSep 13, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5no4
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3663.png

Downloads & links

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Map

FileDownload / File: emd_3663.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.10174256 - 0.30415884
Average (Standard dev.)0.0020510047 (±0.015683318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 355.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z355.840355.840355.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1020.3040.002

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Supplemental data

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Half map: Note calibrated pixel size is 1.39: use this...

Fileemd_3663_half_map_1.map
AnnotationNote calibrated pixel size is 1.39: use this value for post-processing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_3663_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire 30S ribosomal subunit bound by RsgA

EntireName: 30S ribosomal subunit bound by RsgA / Number of components: 24

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Component #1: protein, 30S ribosomal subunit bound by RsgA

ProteinName: 30S ribosomal subunit bound by RsgA / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #2: nucleic-acid, 16S ribosomal RNA

nucleic acidName: 16S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU ...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(G7M)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 AGCUUAACCU UCGGGAGGGC GCUUACCACU UUGUGAUUCA UGACUGGGGU GAAGUCG(UR3)AA CAAGGUAACC GUAGG(2MG)G(MA6)(MA6)C CUGCGGUUGG AUCA
MassTheoretical: 497.404969 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #3: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.078785 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #4: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.383002 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #5: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.361878 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #6: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.326251 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #7: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.54385 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #8: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.015361 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #9: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.554882 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #10: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.325117 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #11: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.4872 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #12: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.641981 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #13: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.625753 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #14: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.475364 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #15: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.159621 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #16: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #17: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.263946 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #18: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.466477 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #19: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.057626 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #20: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.577268 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)

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Component #21: protein, Small ribosomal subunit biogenesis GTPase RsgA

ProteinName: Small ribosomal subunit biogenesis GTPase RsgA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.850457 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #22: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 71 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #23: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #24: ligand, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

LigandName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.522196 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.8
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 95 %

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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: 2.3 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 59000.0 X (nominal), 101000.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3408

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 61908
3D reconstructionSoftware: RELION / Resolution: 5.16 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

5no4

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