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- PDB-6w6p: MultiBody Refinement of 70S Ribosome from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 6w6p
TitleMultiBody Refinement of 70S Ribosome from Enterococcus faecalis
Components
  • (30S ribosomal protein ...) x 18
  • (50S ribosomal protein ...) x 26
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
KeywordsRIBOSOME / 70S / pathogen / antibiotic development / antibiotic resistant
Function / homology
Function and homology information


large ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / zinc ion binding
Ribosomal protein L3, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S13, bacterial-type ...Ribosomal protein L3, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S10, conserved site / Ribosomal protein S11, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein S5, N-terminal / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / K homology domain-like, alpha/beta / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L5, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L17 superfamily / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L5, N-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S18 superfamily / L28p-like / Ribosomal protein L5, C-terminal / Ribosomal protein L34, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein S14, type Z / Ribosomal protein L15 / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L28/L24 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L21-like / Ribosomal protein L25/L23 / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein S3, C-terminal / Ribosomal protein L6 / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L22/L17 / Ribosomal protein L15, conserved site / Ribosomal protein S14 / Ribosomal protein L28 / Ribosomal protein L3 / Ribosomal protein S18 / Ribosomal protein L27 / Ribosomal protein L33 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L21 / Ribosomal protein S10 / Ribosomal protein L29/L35 / Ribosomal protein S8
50S ribosomal protein L20 / 50S ribosomal protein L21 / 50S ribosomal protein L27 / 30S ribosomal protein S5 / 50S ribosomal protein L35 / 50S ribosomal protein L17 / 50S ribosomal protein L30 / 30S ribosomal protein S16 / 50S ribosomal protein L32 / 30S ribosomal protein S4 ...50S ribosomal protein L20 / 50S ribosomal protein L21 / 50S ribosomal protein L27 / 30S ribosomal protein S5 / 50S ribosomal protein L35 / 50S ribosomal protein L17 / 50S ribosomal protein L30 / 30S ribosomal protein S16 / 50S ribosomal protein L32 / 30S ribosomal protein S4 / 50S ribosomal protein L19 / 30S ribosomal protein S20 / 50S ribosomal protein L33 / 30S ribosomal protein S11 / 30S ribosomal protein S15 / 50S ribosomal protein L28 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L34 / un:a0a449dxs1: / 50S ribosomal protein L24 / 50S ribosomal protein L36 / 50S ribosomal protein L29 / 50S ribosomal protein L14 / 30S ribosomal protein S18 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 30S ribosomal protein S12 / 50S ribosomal protein L3 / 30S ribosomal protein S10 / 50S ribosomal protein L2 / 50S ribosomal protein L23 / 30S ribosomal protein S3 / 50S ribosomal protein L5 / 50S ribosomal protein L4 / 30S ribosomal protein S17 / 30S ribosomal protein S8 / 50S ribosomal protein L18 / 30S ribosomal protein S14 type Z / 50S ribosomal protein L15 / 50S ribosomal protein L22 / 30S ribosomal protein S13 / 50S ribosomal protein L16 / 50S ribosomal protein L6 / gb:327533853:
Biological speciesEnterococcus faecalis OG1RF (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsJogl, G. / Khayat, R.
Funding support United States, 2items
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
a: 16S rRNA
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 type Z
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
A: 23S rRNA
B: 5S rRNA
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
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
0: 50S ribosomal protein L30
2: 50S ribosomal protein L32
3: 50S ribosomal protein L33
4: 50S ribosomal protein L34
5: 50S ribosomal protein L35
6: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,046,92851
Polymers2,046,66647
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area216010 Å2
ΔGint-1860 kcal/mol
Surface area782060 Å2

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Components

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RNA chain , 3 types, 3 molecules aAB

#1: RNA chain 16S rRNA


Mass: 501090.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: GenBank: 327533853
#20: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 942675.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: GenBank: 327533853
#21: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 37433.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: GenBank: 327533853

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30S ribosomal protein ... , 18 types, 18 molecules cdefghijklmnopqrst

#2: Protein 30S ribosomal protein S3 /


Mass: 22884.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKR8
#3: Protein 30S ribosomal protein S4 /


Mass: 23029.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XRV7
#4: Protein 30S ribosomal protein S5 /


Mass: 17156.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKW0
#5: Protein 30S ribosomal protein S6 /


Mass: 11331.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKB6
#6: Protein 30S ribosomal protein S7 /


Mass: 17547.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKQ3
#7: Protein 30S ribosomal protein S8 /


Mass: 14805.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKS6
#8: Protein 30S ribosomal protein S9 /


Mass: 14069.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XSA2
#9: Protein 30S ribosomal protein S10 /


Mass: 11400.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKR5
#10: Protein 30S ribosomal protein S11 /


Mass: 12322.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKV1
#11: Protein 30S ribosomal protein S12 /


Mass: 15178.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKQ7
#12: Protein 30S ribosomal protein S13 /


Mass: 12619.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKT7
#13: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7041.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKT0
#14: Protein 30S ribosomal protein S15 /


Mass: 10537.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XRW3
#15: Protein 30S ribosomal protein S16 /


Mass: 10095.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XP69
#16: Protein 30S ribosomal protein S17 /


Mass: 9744.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKS3
#17: Protein 30S ribosomal protein S18 /


Mass: 7646.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKB3
#18: Protein 30S ribosomal protein S19 /


Mass: 8999.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A449DXS1
#19: Protein 30S ribosomal protein S20 /


Mass: 8841.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XQJ7

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50S ribosomal protein ... , 26 types, 26 molecules CDEFGKLMNOPQRSTUVXYZ023456

#22: Protein 50S ribosomal protein L2 /


Mass: 30159.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKR6
#23: Protein 50S ribosomal protein L3 /


Mass: 22498.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKR3
#24: Protein 50S ribosomal protein L4 /


Mass: 22384.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKU7
#25: Protein 50S ribosomal protein L5 /


Mass: 19863.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKS2
#26: Protein 50S ribosomal protein L6 /


Mass: 19164.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKU3
#27: Protein 50S ribosomal protein L13 /


Mass: 16099.585 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XSB2
#28: Protein 50S ribosomal protein L14 /


Mass: 13165.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKS1
#29: Protein 50S ribosomal protein L15 /


Mass: 15602.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKT1
#30: Protein 50S ribosomal protein L16 /


Mass: 15960.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKU1
#31: Protein 50S ribosomal protein L17 /


Mass: 14156.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKX1
#32: Protein 50S ribosomal protein L18 /


Mass: 12806.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKS7
#33: Protein 50S ribosomal protein L19 /


Mass: 13113.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XPL8
#34: Protein 50S ribosomal protein L20 /


Mass: 13542.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XM76
#35: Protein 50S ribosomal protein L21 /


Mass: 11166.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XMC1
#36: Protein 50S ribosomal protein L22 /


Mass: 12126.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKT6
#37: Protein 50S ribosomal protein L23 /


Mass: 10297.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKR7
#38: Protein 50S ribosomal protein L24 /


Mass: 10892.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKV5
#39: Protein 50S ribosomal protein L27 /


Mass: 8146.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XMB1
#40: Protein 50S ribosomal protein L28 /


Mass: 6072.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XRZ8
#41: Protein 50S ribosomal protein L29 /


Mass: 7211.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKV0
#42: Protein 50S ribosomal protein L30 /


Mass: 6234.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKW1
#43: Protein 50S ribosomal protein L32 /


Mass: 6217.372 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XMM2
#44: Protein/peptide 50S ribosomal protein L33 /


Mass: 6052.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XR98
#45: Protein/peptide 50S ribosomal protein L34 /


Mass: 5373.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XSI4
#46: Protein 50S ribosomal protein L35 /


Mass: 7466.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XM73
#47: Protein/peptide 50S ribosomal protein L36 /


Mass: 4440.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKT9

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Non-polymers , 1 types, 4 molecules

#48: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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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: 70S ribosomeRibosome / Type: RIBOSOME / Entity ID: #1-#47 / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Details: Sample was monodisperse. / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
2Leginonimage acquisition
4CTFFIND4CTF correction
7Coot0.8.9.1model fitting
9PHENIX1.14_3235model refinement
10RELION3.1initial Euler assignment
11cryoSPARC0.63final Euler assignment
12FREALIGN9.03classification
13cryoSPARC0.633D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335675 / Symmetry type: POINT
Atomic model buildingB value: 177 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation Coefficient
Atomic model building
IDPDB-ID3D fitting-ID
15LI01
24YBB1
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 17.14 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0099145353
ELECTRON MICROSCOPYf_angle_d1.0669217934
ELECTRON MICROSCOPYf_chiral_restr0.057127945
ELECTRON MICROSCOPYf_plane_restr0.007311316
ELECTRON MICROSCOPYf_dihedral_angle_d16.7968240

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