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- PDB-5kps: Structure of RelA bound to ribosome in absence of A/R tRNA (Struc... -

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Basic information

Entry
Database: PDB / ID: 5kps
TitleStructure of RelA bound to ribosome in absence of A/R tRNA (Structure I)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • E-site tRNAfMet
  • GTP pyrophosphokinase
  • P site tRNAfmet
  • mRNAMessenger RNA
KeywordsRIBOSOME / ribosome / RelA
Function / homologyRibosomal protein S4/S9 / Ribosomal protein L5, 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 S6, conserved site ...Ribosomal protein S4/S9 / Ribosomal protein L5, 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 S6, conserved site / Ribosomal protein L35 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L16, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S9, conserved site / Ribosomal protein L28/L24 / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein L10 / 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 S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S16, conserved site / Ribosomal protein S5 domain 2-type fold / RelA, TGS domain / Ribosomal protein S4, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein L30, ferredoxin-like fold domain / K homology domain-like, alpha/beta / Ribosomal protein L2, domain 3 / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L27, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L9, N-terminal / Ribosomal protein S17, conserved site / Ribosomal protein L9, C-terminal / 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 L14P, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein L5, N-terminal / L28p-like / Ribosomal protein L25/L23 / Ribosomal protein S17 / Ribosomal protein L10 / Ribosomal protein L20 / Ribosomal protein L36 / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein L6 / Ribosomal protein L34 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L3 / KOW motif
Function and homology information
Specimen sourceEscherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsLoveland, A.B. / Bah, E. / Madireddy, R. / Zhang, Y. / Brilot, A.F. / Grigorieff, N. / Korostelev, A.A.
CitationJournal: Elife / Year: 2016
Title: Ribosome•RelA structures reveal the mechanism of stringent response activation.
Authors: Anna B Loveland / Eugene Bah / Rohini Madireddy / Ying Zhang / Axel F Brilot / Nikolaus Grigorieff / Andrei A Korostelev
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 5, 2016 / Release: Sep 28, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 28, 2016Structure modelrepositoryInitial release
1.1Sep 13, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization
1.2Nov 22, 2017Structure modelDatabase references / Experimental preparationcitation / em_sample_support_citation.title / _em_sample_support.grid_type
1.3Jul 18, 2018Structure modelData collectionem_software_em_software.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: GTP pyrophosphokinase
B: 50S ribosomal protein L2
C: 50S ribosomal protein L3
D: 50S ribosomal protein L4
E: 50S ribosomal protein L5
F: 50S ribosomal protein L6
G: 50S ribosomal protein L9
H: 50S ribosomal protein L10
I: 50S ribosomal protein L11
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
1: 50S ribosomal protein L31
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
7: 30S ribosomal protein S2
8: 30S ribosomal protein S3
9: 30S ribosomal protein S4
10: 30S ribosomal protein S5
11: 30S ribosomal protein S6
12: 30S ribosomal protein S7
13: 30S ribosomal protein S8
14: 30S ribosomal protein S9
15: 30S ribosomal protein S10
16: 30S ribosomal protein S11
17: 30S ribosomal protein S12
18: 30S ribosomal protein S13
19: 30S ribosomal protein S14
20: 30S ribosomal protein S15
21: 30S ribosomal protein S16
22: 30S ribosomal protein S17
23: 30S ribosomal protein S18
24: 30S ribosomal protein S19
25: 30S ribosomal protein S20
26: 30S ribosomal protein S21
27: 16S ribosomal RNA
28: 23S ribosomal RNA
29: 5S ribosomal RNA
30: mRNA
31: P site tRNAfmet
32: E-site tRNAfMet


Theoretical massNumber of molelcules
Total (without water)2,311,71658
Polyers2,311,71658
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide GTP pyrophosphokinase / (p)ppGpp synthase / ATP:GTP 3'-pyrophosphotransferase / ppGpp synthase I


Mass: 84825.508 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: relA, b2784, JW2755 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0AG20, GTP diphosphokinase

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50S ribosomal protein ... , 31 types, 31 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ123456

#2: Protein/peptide 50S ribosomal protein L2 /


Mass: 29923.619 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60422
#3: Protein/peptide 50S ribosomal protein L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60438
#4: Protein/peptide 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60723
#5: Protein/peptide 50S ribosomal protein L5 /


Mass: 20333.611 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P62399
#6: Protein/peptide 50S ribosomal protein L6 /


Mass: 18932.791 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG55
#7: Protein/peptide 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R1
#8: Protein/peptide 50S ribosomal protein L10 / / 50S ribosomal protein L8


Mass: 17736.596 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7J3
#9: Protein/peptide 50S ribosomal protein L11 /


Mass: 14894.362 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7J7
#10: Protein/peptide 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AA10
#11: Protein/peptide 50S ribosomal protein L14 /


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADY3
#12: Protein/peptide 50S ribosomal protein L15 /


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02413
#13: Protein/peptide 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADY7
#14: Protein/peptide 50S ribosomal protein L17 /


Mass: 14393.657 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG44
#15: Protein/peptide 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0C018
#16: Protein/peptide 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7K6
#17: Protein/peptide 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7L3
#18: Protein/peptide 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG48
#19: Protein/peptide 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P61175
#20: Protein/peptide 50S ribosomal protein L23 /


Mass: 11222.160 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADZ0
#21: Protein/peptide 50S ribosomal protein L24 /


Mass: 11339.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60624
#22: Protein/peptide 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P68919
#23: Protein/peptide 50S ribosomal protein L27 /


Mass: 9146.540 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7L8
#24: Protein/peptide 50S ribosomal protein L28 /


Mass: 9027.551 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7M2
#25: Protein/peptide 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7M6
#26: Protein/peptide 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG51
#27: Protein/peptide 50S ribosomal protein L31 /


Mass: 7887.117 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7M9
#28: Protein/peptide 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7N4
#29: Protein/peptide 50S ribosomal protein L33 /


Mass: 6388.631 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7N9
#30: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7P5
#31: Protein/peptide 50S ribosomal protein L35 / / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7Q1
#32: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7Q6

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30S ribosomal protein ... , 20 types, 20 molecules 7891011121314151617181920212223242526

#33: Protein/peptide 30S ribosomal protein S2 /


Mass: 26781.670 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V0
#34: Protein/peptide 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V3
#35: Protein/peptide 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V8
#36: Protein/peptide 30S ribosomal protein S5 /


Mass: 17629.398 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7W1
#37: Protein/peptide 30S ribosomal protein S6 /


Mass: 15727.512 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02358
#38: Protein/peptide 30S ribosomal protein S7 /


Mass: 20055.156 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02359
#39: Protein/peptide 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7W7
#40: Protein/peptide 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7X3
#41: Protein/peptide 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R5
#42: Protein/peptide 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R9
#43: Protein/peptide 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7S3
#44: Protein/peptide 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7S9
#45: Protein/peptide 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG59
#46: Protein/peptide 30S ribosomal protein S15 /


Mass: 10290.816 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADZ4
#47: Protein/peptide 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7T3
#48: Protein/peptide 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG63
#49: Protein/peptide 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7T7
#50: Protein/peptide 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7U3
#51: Protein/peptide 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7U7
#52: Protein/peptide 30S ribosomal protein S21 /


Mass: 8524.039 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P68679

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RNA chain , 6 types, 6 molecules 272829303132

#53: RNA chain 16S ribosomal RNA /


Mass: 498725.406 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 731469900
#54: RNA chain 23S ribosomal RNA /


Mass: 941321.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 802133627
#55: RNA chain 5S ribosomal RNA /


Mass: 38813.133 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1028475309
#56: RNA chain mRNA / Messenger RNA


Mass: 5844.563 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli K-12 (bacteria)
#57: RNA chain P site tRNAfmet


Mass: 24802.785 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1043194029
#58: RNA chain E-site tRNAfMet


Mass: 24786.785 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 731469900

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: RelA bound to 70S ribosome in the absence of A/R tRNA / Type: RIBOSOME
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58
Source: MULTIPLE SOURCES
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 75 % / Chamber temperature: 295 kelvins
Details: Apply 2 uL sample and blot 4 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 30488 / Calibrated magnification: 30488 / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.4 sec. / Electron dose: 1.6 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 5 / Number of real images: 5763
Image scansMovie frames/image: 25 / Used frames/image: 1-25

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Processing

EM software
IDNameVersionCategory
1Signaturelinux64_patchedparticle selection
2SerialEMimage acquisition
4CTFFIND3CTF correction
5FREALIGN9.07-9.12CTF correction
8UCSF Chimeramodel fitting
9PyMOLmodel fitting
11CNS-RSREFmodel refinement
12FREALIGN9.07-9.12initial Euler assignment
13FREALIGN9.07-9.12final Euler assignment
14FREALIGN9.07-9.12classification
15FREALIGN9.07-9.123D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 564385
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 76158 / Number of class averages: 1 / Symmetry type: POINT

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