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- EMDB-6789: Large subunit of Mycobacterium smegmatis -

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Basic information

Entry
Database: EMDB / ID: 6789
TitleLarge subunit of Mycobacterium smegmatis
SampleLarge subunit of Mycobacterium smegmatis ribosome
SourceMycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Map data
Methodsingle particle reconstruction, at 3.08 Å resolution
AuthorsLi Z / Ge X
CitationProtein Cell, 2017

Protein Cell, 2017 Yorodumi Papers
Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers.
Zhifei Li / Xueliang Ge / Yixiao Zhang / Lvqin Zheng / Suparna Sanyal / Ning Gao

Validation ReportPDB-ID: 5xym

SummaryFull reportAbout validation report
DateDeposition: Jul 9, 2017 / Header (metadata) release: Sep 27, 2017 / Map release: Sep 27, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.044
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.044
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5xym
  • Surface level: 0.044
  • Imaged by UCSF CHIMERA
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3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_6789.map.gz (map file in CCP4 format, 87809 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
280 pix
1.32 Å/pix.
= 369.6 Å
280 pix
1.32 Å/pix.
= 369.6 Å
280 pix
1.32 Å/pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.044 (by author), 0.044 (movie #1):
Minimum - Maximum-0.24304397 - 0.39521706
Average (Standard dev.)0.00076097535 (0.012051829)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions280280280
Origin000
Limit279279279
Spacing280280280
CellA=B=C: 369.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z369.600369.600369.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.2430.3950.001

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Supplemental data

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Sample components

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Entire Large subunit of Mycobacterium smegmatis ribosome

EntireName: Large subunit of Mycobacterium smegmatis ribosome / Number of components: 33

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Component #1: protein, Large subunit of Mycobacterium smegmatis ribosome

ProteinName: Large subunit of Mycobacterium smegmatis ribosome / Recombinant expression: No
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #2: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Recombinant expression: No
MassTheoretical: 6.467719 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #3: protein, 50S ribosomal protein L33 2

ProteinName: 50S ribosomal protein L33 2 / Recombinant expression: No
MassTheoretical: 6.61564 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #4: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Recombinant expression: No
MassTheoretical: 5.52258 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #5: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Recombinant expression: No
MassTheoretical: 7.298505 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #6: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Recombinant expression: No
MassTheoretical: 4.341277 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #7: nucleic-acid, 23S RNA

Nucleic-acidName: 23S RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUGUAAGUGU UUAAGGGCGC AUGGUGGAUG CCUUGGCACU GGGAGCCGAU GAAGGACGUA GGAGGCUGCG AUAAGCCUCG GGGAGCUGUC AACCGAGCGU UGAUCCGAGG AUGUCCGAAU GGGGAAACCC GGCACGAGUG AUGUCGUGUC ACCAGGCGCU GAAUAUAUAG GCGUCUGGGG GGAACGCGGG GAAGUGAAAC AUCUCAGUAC CCGUAGGAAG AGAAAACAAA AUGUGAUUCC GUGAGUAGUG GCGAGCGAAA GCGGAGGAUG GCUAAACCGU AUGCAUGUGA UACCGGGUAG GGGUUGUGUG UGCGGGGUUG UGGGACCUAU CUUUCCGGCU CUACCUGGCU GGAGGGCAGU GAGAAAAUGU UGUGGUUAGC GGAAAUGGCU UGGGAUGGCC UGCCGUAGAC GGUGAGAGCC CGGUACGUGA AAACCCGACG UCUGUCUUGA UGGUGUUCCC GAGUAGCAGC GGGCCCGUGG AAUCUGCUGU GAAUCUGCCG GGACCACCCG GUAAGCCUGA AUACUUCCCA GUGACCGAUA GCGGAUUAGU ACCGUGAGGG AAUGGUGAAA AGUACCCCGG GAGGGGAGUG AAAGAGUACC UGAAACCGUG CGCUUACAAU CCGUCAGAGC CCUCGACGUG UCGUGGGGUG AUGGCGUGCC UUUUGAAGAA UGAGCCUGCG AGUCAGGGAC AUGUCGCGAG GUUAACCCGG GUGGGGUAGC CGCAGCGAAA GCGAGUCUGA AUAGGGCGUA UCCACACAAG AGUGUGUGGU GUAGUGGUGU GUUCUGGACC CGAAGCGGAG UGAUCUACCC AUGGCCAGGG UGAAGCGCGG GUAAGACCGC GUGGAGGCCC GAACCCACUU AGGUUGAAGA CUGAGGGGAU GAGCUGUGGG UAGGGGUGAA AGGCCAAUCA AACUCCGUGA UAGCUGGUUC UCCCCGAAAU GCAUUUAGGU GCAGCGUCGC AUGUUUCUUG CCGGAGGUAG AGCUACUGGA UGGCCGAUGG GCCCCACAGG GUUACUGACG UCAGCCAAAC UCCGAAUGCC GGUAAGUCCA AGAGUGCGGC AGUGGGACGG CGGGGGAUAA GCUCCGUGCG UCGAGAGGGA AACAGCCCAG AUCGCCGGCU AAGGCCCCUA AGCGUGUGCU AAGUGGAAAA GGAUGUGCAG UCGCGAAGAC AACCAGGAGG UUGGCUUAGA AGCAGCCACC CUUGAAAGAG UGCGUAAUAG CUCACUGGUC AAGUGAUUGU GCGCCGAUAA UGUAGCGGGG CUCAAGCACA CCGCCGAAGC CGCGGCAGCC AACGUGUUGG CUGGGUAGGG GAGCGUCCUG CAUCCGGUGA AGCCGCCGAG UGAUCGAGUG GUGGAGGGUG UGGGAGUGAG AAUGCAGGCA UGAGUAGCGA UUAGGCAAGU GAGAACCUUG CCCGCCGAAA GACCAAGGGU UCCUGGGCCA GGCCAGUCCG CCCAGGGUGA GUCGGGACCU AAGGCGAGGC CGACAGGCGU AGUCGAUGGA CAACGGGUUG AUAUUCCCGU ACCCGUGUAU GUGCGUCCAU GAUGAAUCAG CGGUACUAAC CAUCCAAAAC CACCGUGACC GCACCUUUCG GGGUGUGGCG UUGGUGGGGC UGCAUGGGAC CUUCGUUGGU AGUAGUCAAG CGAUGGGGUG ACGCAGGAAG GUAGCCGUAC CGGUCAGUGG UAAUACCGGG GUAAGCCUGU AGGGAGUCAG AUAGGUAAAU CCGUCUGGCA UAUAUCCUGA GAGGUGAUGC AUAGCCGAGU GAGGCGAAUU CGGUGAUCCU AUGCUGCCGA GAAAAGCCUC UAGCGAGGAC AUACACGGCC CGUACCCCAA ACCAACACAG GUGGUCAGGU AGAGAAUACU AAGGCGUACG AGUGAACUAU GGUUAAGGAA CUCGGCAAAA UGCCCCCGUA ACUUCGGGAG AAGGGGGACC CACAUGGCGU GUAAGCCUUU ACGGCCCAAG CGUGAGUGGG UGGCACAAAC CAGUGAGAAG CGACUGUUUA CUAAAAACAC AGGUCCGUGC GAAGUCGCAA GACGAUGUAU ACGGACUGAC GCCUGCCCGG UGCUGGAAGG UUAAGAGGAC CCGUUAACUC CCUUUGGGGG UGAAGCGGAG AAUUUAAGCC CCAGUAAACG GCGGUGGUAA CUAUAACCAU CCUAAGGUAG CGAAAUUCCU UGUCGGGUAA GUUCCGACCU GCACGAAUGG CGUAACGACU UCUCAACUGU CUCAACCAUA GACUCGGCGA AAUUGCACUA CGAGUAAAGA UGCUCGUUAC GCGCGGCAGG ACGAAAAGAC CCCGGGACCU UCACUACAAC UUGGUAUUGG UGCUCGAUAC GGUUUGUGUA GGAUAGGUGG GAGACUGUGA AGCUCACACG CCAGUGUGGG UGGAGUCGUU GUUGAAAUAC CACUCUGAUC GUAUUGGGCC UCUAACCUCG GACCGUAUAU CCGGUUCAGG GACAGUGCCU GGUGGGUAGU UUAACUGGGG CGGUUGCCUC CUAAAAUGUA ACGGAGGCGC CCAAAGGUUC CCUCAACCUG GACGGCAAUC AGGUGUUGAG UGUAAGUGCA CAAGGGAGCU UGACUGCGAG ACGGACAUGU CGAGCAGGGA CGAAAGUCGG GACUAGUGAU CCGGCACCUC UGAGUGGAAG GGGUGUCGCU CAACGGAUAA AAGGUACCCC GGGGAUAACA GGCUGAUCUU CCCCAAGAGU CCAUAUCGAC GGGAUGGUUU GGCACCUCGA UGUCGGCUCG UCGCAUCCUG GGGCUGGAGC AGGUCCCAAG GGUUGGGCUG UUCGCCCAUU AAAGCGGCAC GCGAGCUGGG UUUAGAACGU CGUGAGACAG UUCGGUCUCU AUCCGCCGCG CGCGUCAGAA GCUUGAGGAA ACCUGUCCCU AGUACGAGAG GACCGGGACG GACGAACCUC UGGUAUACCA GUUGUCCCAC CAGGGGCACG GCUGGAUAGC CACGUUCGGA CAGGAUAACC GCUGAAAGCA UCUAAGCGGG AAACCUCUUC CAAGACCAGG CUUCUCACCC UCUAGGAGGG AUAAGGCCCC CCGCAGACCA CGGGAUUGAU AGACCAGACC UGGAAGCCUA GUAAUAGGUG CAGGGAACUG GCACUAACCG GCCGAAAACU UACAACACCC CAUAAUCGUU GUAAGAAGAA AACAUUGACG CACC
MassTheoretical: 1.026283438 MDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #8: nucleic-acid, 5S RNA

Nucleic-acidName: 5S RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUACGGCGG UCCAUAGCGG CAGGGAAACG CCCGGUCCCA UCCCGAACCC GGAAGCUAAG CCUGCCAGCG CCGAUGAUAC UACCCUUCCG GGUGGAAAAG UAGGACACCG CCGAACAC
MassTheoretical: 38.038777 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #9: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Recombinant expression: No
MassTheoretical: 30.425945 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #10: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Recombinant expression: No
MassTheoretical: 23.011393 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #11: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Recombinant expression: No
MassTheoretical: 22.920949 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #12: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Recombinant expression: No
MassTheoretical: 21.152328 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #13: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Recombinant expression: No
MassTheoretical: 19.483361 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #14: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Recombinant expression: No
MassTheoretical: 15.949253 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #15: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Recombinant expression: No
MassTheoretical: 16.146689 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #16: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Recombinant expression: No
MassTheoretical: 13.400625 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #17: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Recombinant expression: No
MassTheoretical: 15.602244 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #18: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Recombinant expression: No
MassTheoretical: 15.77424 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #19: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Recombinant expression: No
MassTheoretical: 21.892246 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #20: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Recombinant expression: No
MassTheoretical: 13.711728 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #21: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Recombinant expression: No
MassTheoretical: 12.892806 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #22: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Recombinant expression: No
MassTheoretical: 14.494693 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #23: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Recombinant expression: No
MassTheoretical: 11.055894 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #24: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Recombinant expression: No
MassTheoretical: 16.3536 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #25: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Recombinant expression: No
MassTheoretical: 11.047836 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #26: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Recombinant expression: No
MassTheoretical: 11.228946 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #27: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Recombinant expression: No
MassTheoretical: 22.571078 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #28: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Recombinant expression: No
MassTheoretical: 9.249582 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #29: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Recombinant expression: No
MassTheoretical: 6.891016 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #30: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Recombinant expression: No
MassTheoretical: 8.790895 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #31: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Recombinant expression: No
MassTheoretical: 7.022147 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #32: protein, Uncharacterized protein bL37

ProteinName: Uncharacterized protein bL37 / Recombinant expression: No
MassTheoretical: 2.841375 kDa
SourceSpecies: Mycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
Strain: ATCC 700084 / mc(2)155

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Component #33: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 146 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE

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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 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 71351
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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