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- PDB-7uvy: A. baumannii ribosome-Streptothricin-D complex: 70S with P-site tRNA -

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Basic information

Entry
Database: PDB / ID: 7uvy
TitleA. baumannii ribosome-Streptothricin-D complex: 70S with P-site tRNA
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16s Ribosomal RNA
  • 23s ribosomal RNA
  • 5s ribosomal RNA
  • mRNA
  • tRNA-met
KeywordsRibosome/RNA / Streptothricin / Nourseothricin / Antibiotic / Ribosome / Ribosome-RNA complex
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly ...ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / : ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein L20 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / : / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L21
Similarity search - Domain/homology
Streptothricin D / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / 30S ribosomal protein S10 ...Streptothricin D / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / 30S ribosomal protein S10 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL20
Similarity search - Component
Biological speciesAcinetobacter baumannii AB0057 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsMorgan, C.E. / Yu, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: PLoS Biol / Year: 2023
Title: Streptothricin F is a bactericidal antibiotic effective against highly drug-resistant gram-negative bacteria that interacts with the 30S subunit of the 70S ribosome.
Authors: Christopher E Morgan / Yoon-Suk Kang / Alex B Green / Kenneth P Smith / Matthew G Dowgiallo / Brandon C Miller / Lucius Chiaraviglio / Katherine A Truelson / Katelyn E Zulauf / Shade ...Authors: Christopher E Morgan / Yoon-Suk Kang / Alex B Green / Kenneth P Smith / Matthew G Dowgiallo / Brandon C Miller / Lucius Chiaraviglio / Katherine A Truelson / Katelyn E Zulauf / Shade Rodriguez / Anthony D Kang / Roman Manetsch / Edward W Yu / James E Kirby /
Abstract: The streptothricin natural product mixture (also known as nourseothricin) was discovered in the early 1940s, generating intense initial interest because of excellent gram-negative activity. Here, we ...The streptothricin natural product mixture (also known as nourseothricin) was discovered in the early 1940s, generating intense initial interest because of excellent gram-negative activity. Here, we establish the activity spectrum of nourseothricin and its main components, streptothricin F (S-F, 1 lysine) and streptothricin D (S-D, 3 lysines), purified to homogeneity, against highly drug-resistant, carbapenem-resistant Enterobacterales (CRE) and Acinetobacter baumannii. For CRE, the MIC50 and MIC90 for S-F and S-D were 2 and 4 μM, and 0.25 and 0.5 μM, respectively. S-F and nourseothricin showed rapid, bactericidal activity. S-F and S-D both showed approximately 40-fold greater selectivity for prokaryotic than eukaryotic ribosomes in in vitro translation assays. In vivo, delayed renal toxicity occurred at >10-fold higher doses of S-F compared with S-D. Substantial treatment effect of S-F in the murine thigh model was observed against the otherwise pandrug-resistant, NDM-1-expressing Klebsiella pneumoniae Nevada strain with minimal or no toxicity. Cryo-EM characterization of S-F bound to the A. baumannii 70S ribosome defines extensive hydrogen bonding of the S-F steptolidine moiety, as a guanine mimetic, to the 16S rRNA C1054 nucleobase (Escherichia coli numbering) in helix 34, and the carbamoylated gulosamine moiety of S-F with A1196, explaining the high-level resistance conferred by corresponding mutations at the residues identified in single rrn operon E. coli. Structural analysis suggests that S-F probes the A-decoding site, which potentially may account for its miscoding activity. Based on unique and promising activity, we suggest that the streptothricin scaffold deserves further preclinical exploration as a potential therapeutic for drug-resistant, gram-negative pathogens.
History
DepositionMay 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: 50S ribosomal protein L33
1: 50S ribosomal protein L34
2: 50S ribosomal protein L35
3: 50S ribosomal protein L36
A: 23s ribosomal RNA
B: 5s ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L13
J: 50S ribosomal protein L14
K: 50S ribosomal protein L15
L: 50S ribosomal protein L16
M: 50S ribosomal protein L17
N: 50S ribosomal protein L18
O: 50S ribosomal protein L19
P: 50S ribosomal protein L20
Q: 50S ribosomal protein L21
R: 50S ribosomal protein L22
S: 50S ribosomal protein L23
T: 50S ribosomal protein L24
U: 50S ribosomal protein L25
V: 50S ribosomal protein L27
W: 50S ribosomal protein L28
X: 50S ribosomal protein L29
Y: 50S ribosomal protein L30
Z: 50S ribosomal protein L32
a: 16s Ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
u: 30S ribosomal protein S21
v: tRNA-met
w: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,169,99167
Polymers2,160,79553
Non-polymers9,19614
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 28 types, 28 molecules 0123CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein 50S ribosomal protein L33


Mass: 6105.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: A0A7U4DFF9
#2: Protein/peptide 50S ribosomal protein L34


Mass: 5192.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A1J6Y3G0
#3: Protein 50S ribosomal protein L35


Mass: 7424.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I693
#4: Protein/peptide 50S ribosomal protein L36


Mass: 4276.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA18
#7: Protein 50S ribosomal protein L2


Mass: 30346.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA36
#8: Protein 50S ribosomal protein L3


Mass: 22512.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA39
#9: Protein 50S ribosomal protein L4


Mass: 21583.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA38
#10: Protein 50S ribosomal protein L5


Mass: 20051.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA27
#11: Protein 50S ribosomal protein L6


Mass: 19126.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA24
#12: Protein 50S ribosomal protein L9


Mass: 15800.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IBC3
#13: Protein 50S ribosomal protein L13


Mass: 15981.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I9B0
#14: Protein 50S ribosomal protein L14


Mass: 13523.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: N8SHC6
#15: Protein 50S ribosomal protein L15


Mass: 15509.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA20
#16: Protein 50S ribosomal protein L16


Mass: 15498.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA32
#17: Protein 50S ribosomal protein L17


Mass: 14022.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA13
#18: Protein 50S ribosomal protein L18


Mass: 12443.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA23
#19: Protein 50S ribosomal protein L19


Mass: 13619.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IAS9
#20: Protein 50S ribosomal protein L20


Mass: 13468.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: V5VGC9
#21: Protein 50S ribosomal protein L21


Mass: 11496.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I6V9
#22: Protein 50S ribosomal protein L22


Mass: 11828.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A009I821
#23: Protein 50S ribosomal protein L23


Mass: 11607.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA37
#24: Protein 50S ribosomal protein L24


Mass: 11187.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA28
#25: Protein 50S ribosomal protein L25


Mass: 10942.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I7B6
#26: Protein 50S ribosomal protein L27


Mass: 9072.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I6V8
#27: Protein 50S ribosomal protein L28


Mass: 9125.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: N9N7A0
#28: Protein 50S ribosomal protein L29


Mass: 7449.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA31
#29: Protein 50S ribosomal protein L30


Mass: 6654.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA21
#30: Protein 50S ribosomal protein L32


Mass: 7096.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I7A4

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RNA chain , 5 types, 5 molecules ABavw

#5: RNA chain 23s ribosomal RNA


Mass: 945315.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria)
#6: RNA chain 5s ribosomal RNA


Mass: 36996.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: GenBank: 1577037162
#31: RNA chain 16s Ribosomal RNA


Mass: 500297.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: GenBank: 1211343212
#52: RNA chain tRNA-met


Mass: 24760.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: GenBank: 1723902888
#53: RNA chain mRNA


Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria)

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30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu

#32: Protein 30S ribosomal protein S2


Mass: 27680.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: V5VBC2
#33: Protein 30S ribosomal protein S3


Mass: 27972.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: V5V9N0
#34: Protein 30S ribosomal protein S4


Mass: 23311.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA15
#35: Protein 30S ribosomal protein S5


Mass: 17181.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA22
#36: Protein 30S ribosomal protein S6


Mass: 14986.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IBC1
#37: Protein 30S ribosomal protein S7


Mass: 17733.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I7S0
#38: Protein 30S ribosomal protein S8


Mass: 14250.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA25
#39: Protein 30S ribosomal protein S9


Mass: 14287.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: V5VBA5
#40: Protein 30S ribosomal protein S10


Mass: 11718.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A009L7S8
#41: Protein 30S ribosomal protein S11


Mass: 13558.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A4R0F9S8
#42: Protein 30S ribosomal protein S12


Mass: 13797.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I7R9
#43: Protein 30S ribosomal protein S13


Mass: 13295.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA17
#44: Protein 30S ribosomal protein S14


Mass: 11438.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA26
#45: Protein 30S ribosomal protein S15


Mass: 10145.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I3U0
#46: Protein 30S ribosomal protein S16


Mass: 11223.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A1V3DIZ9
#47: Protein 30S ribosomal protein S17


Mass: 9543.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA30
#48: Protein 30S ribosomal protein S18


Mass: 9009.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A372MP10
#49: Protein 30S ribosomal protein S19


Mass: 10206.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA35
#50: Protein 30S ribosomal protein S20


Mass: 9723.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I5N9
#51: Protein 30S ribosomal protein S21


Mass: 8474.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A0Q7FMS9

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Non-polymers , 4 types, 19 molecules

#54: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#55: Chemical
ChemComp-OIY / Streptothricin D


Mass: 758.867 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C31H58N12O10 / Feature type: SUBJECT OF INVESTIGATION
#56: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#57: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SD-70S Ribosome Complex with P-site tRNA / Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL
Source (natural)Organism: Acinetobacter baumannii AB0057 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19_4080: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144189 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004150889
ELECTRON MICROSCOPYf_angle_d0.621225738
ELECTRON MICROSCOPYf_dihedral_angle_d14.57859467
ELECTRON MICROSCOPYf_chiral_restr0.03928914
ELECTRON MICROSCOPYf_plane_restr0.00612064

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