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- EMDB-6789: Large subunit of Mycobacterium smegmatis -

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Basic information

Entry
Database: EMDB / ID: EMD-6789
TitleLarge subunit of Mycobacterium smegmatis
Map data
Sample
  • Complex: Large subunit of Mycobacterium smegmatis ribosome
    • Protein or peptide: x 29 types
    • RNA: x 2 types
  • Ligand: x 1 types
KeywordsMycobacterium smegmatis ribosome / rRNA / rprotein / RIBOSOME
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / cytoplasm
Similarity search - Function
: / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. ...: / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / 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 L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site
Similarity search - Domain/homology
Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 ...Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Uncharacterized protein / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33B / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesMycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsLi Z / Ge X
CitationJournal: Protein Cell / Year: 2018
Title: Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers.
Authors: Zhifei Li / Xueliang Ge / Yixiao Zhang / Lvqin Zheng / Suparna Sanyal / Ning Gao /
History
DepositionJul 9, 2017-
Header (metadata) releaseSep 27, 2017-
Map releaseSep 27, 2017-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.044
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.044
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5xym
  • Surface level: 0.044
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6789.png

Downloads & links

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Map

FileDownload / File: emd_6789.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.044 / Movie #1: 0.044
Minimum - Maximum-0.24304397 - 0.39521706
Average (Standard dev.)0.00076097535 (±0.012051829)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: Large subunit of Mycobacterium smegmatis ribosome
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33 2
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
    • RNA: 23S RNA
    • RNA: 5S RNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: Uncharacterized protein bL37
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Large subunit of Mycobacterium smegmatis ribosome

SupramoleculeName: Large subunit of Mycobacterium smegmatis ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#31
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Macromolecule #1: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 6.467719 KDa
SequenceString:
MAVPKRRMSR ANTRSRRAQW KAEAPGLVTV SVAGQQRKVP RRLLKAARLG LVDLDKR

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #2: 50S ribosomal protein L33 2

MacromoleculeName: 50S ribosomal protein L33 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 6.61564 KDa
SequenceString:
MARNEIRPIV KLRSTAGTGY TYVTRKNRRN DPDRIVLRKY DPVLRRHVEF REER

UniProtKB: Large ribosomal subunit protein bL33B

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Macromolecule #3: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 5.52258 KDa
SequenceString:
MAKGKRTFQP NNRRRARVHG FRLRMRTRAG RAIVANRRSK GRRALTA

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #4: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 7.298505 KDa
SequenceString:
MPKAKTHSGA SKRFRRTGTG KIVRQKANRR HLLEHKPTKR TRRLDGRTTV SAADNSRINK LLNG

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #5: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 4.341277 KDa
SequenceString:
MKVNPSVKPI CDKCRVIRRH GRVMVICSDP RHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #8: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 30.425945 KDa
SequenceString: MGIRKYKPTT PGRRGASVSD FAEITRSTPE KSLVRPLHGK GGRNAHGRIT TRHKGGGHKR AYRVIDFRRH DKDGVNAKVA HIEYDPNRT ANIALLHYLD GEKRYIIAPQ GLKQGDVIES GANADIKPGN NLPLRNIPAG TVIHAVELRP GGGAKLARSA G VSIQLLGK ...String:
MGIRKYKPTT PGRRGASVSD FAEITRSTPE KSLVRPLHGK GGRNAHGRIT TRHKGGGHKR AYRVIDFRRH DKDGVNAKVA HIEYDPNRT ANIALLHYLD GEKRYIIAPQ GLKQGDVIES GANADIKPGN NLPLRNIPAG TVIHAVELRP GGGAKLARSA G VSIQLLGK EGTYAALRMP SGEIRRVDVR CRATVGEVGN AEQSNINWGK AGRMRWKGKR PTVRGVVMNP VDHPHGGGEG KT SGGRHPV SPWGKPEGRT RKPNKPSDKL IVRRRRTGKK R

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #9: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 23.011393 KDa
SequenceString: MARKGILGTK LGMTQVFDEN NKVVPVTVVK AGPNVVTRIR TTERDGYSAV QLAYGEISPR KVIKPVAGQF AAAGVNPRRH VAELRLDDE AAVAEYEVGQ ELTAEIFSDG AYVDVTGTSK GKGFAGTMKR HGFRGQGAAH GAQAVHRRPG SIGGCATPGR V FKGTRMSG ...String:
MARKGILGTK LGMTQVFDEN NKVVPVTVVK AGPNVVTRIR TTERDGYSAV QLAYGEISPR KVIKPVAGQF AAAGVNPRRH VAELRLDDE AAVAEYEVGQ ELTAEIFSDG AYVDVTGTSK GKGFAGTMKR HGFRGQGAAH GAQAVHRRPG SIGGCATPGR V FKGTRMSG RMGNDRVTTQ NLKVHKVDAE NGVLLIKGAI PGRNGGLVVV RSAIKRGEK

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #10: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 22.920949 KDa
SequenceString: MTLKVDVKTP AGKTDGSVEL PAELFDVEPN IALMHQVVTA QLAAKRQGTH STKTRGEVSG GGKKPYRQKG TGRARQGSTR APQFTGGGT VHGPKPRDYS QRTPKKMIAA ALRGALSDRA RNDRIHAVTE LVEGQTPSTK SAKTFLGTLT ENKKVLVVIG R TDEVGAKS ...String:
MTLKVDVKTP AGKTDGSVEL PAELFDVEPN IALMHQVVTA QLAAKRQGTH STKTRGEVSG GGKKPYRQKG TGRARQGSTR APQFTGGGT VHGPKPRDYS QRTPKKMIAA ALRGALSDRA RNDRIHAVTE LVEGQTPSTK SAKTFLGTLT ENKKVLVVIG R TDEVGAKS VRNLPGVHVI SPDQLNTYDV LNADDVVFSV EALNAYISAN SKEGASV

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #11: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 21.152328 KDa
SequenceString:
MTTTEKALPR LKQRYREEIR EALQQEFNYA NVMQIPGVVK VVVNMGVGDA ARDAKLINGA INDLALITGQ KPEVRRARKS IAQFKLREG MPIGARVTLR GDRMWEFLDR LISIALPRIR DFRGLSPKQF DGTGNYTFGL NEQSMFHEID VDSIDRPRGM D ITVVTTAT NDAEGRALLR ALGFPFKEN

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #12: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 19.483361 KDa
SequenceString:
MSRIGKQPVP VPSGVDVTIN GQNLSVKGPK GTLTLDVAEP ISVSRAEDGA IVVTRPDDER RSRSLHGLSR TLIANLVTGV TEGYTQKME IFGVGYRVQL KGQNLEFALG YSHPVLIEAP EGITFAVESP TKFSVSGIDK QKVGQISAVI RRLRRPDPYK G KGVRYEGE QIRRKVGKTG K

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #13: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 15.949253 KDa
SequenceString:
MKLILTAEVE HLGAAGDTVE VKDGYGRNYL LPRGLAIVAS RGAERQAEEI RRARESKVIR DIEHANELKT ALEGLGDVTL SVNAAGDTG KLFGSVTAAD VVNAIKKAGG PNLDKRTVQL AKAHIKSVGT HPVTVKLHTG VEAKVSLNVV AQ

UniProtKB: Large ribosomal subunit protein bL9

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Macromolecule #14: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 16.146689 KDa
SequenceString:
MPTYTPKAGD TTRSWYVIDA SDVVLGRLAS AAATLLRGKH KPTFTPNVDG GDFVIVINAD KIAVSGDKLT KKFAYRHSGY PGGLRKRTI GELLEKHPTR VVENAIIGML PHNKLGRQIQ KKLKVYAGPD HPHAAQQPIP FEIKQVAQ

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #15: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.400625 KDa
SequenceString:
MIQQESRLKV ADNTGAKEIL CIRVLGGSSR RYAGIGDVIV ATVKDAIPGG NVKRGDVVKA VVVRTVKERR RADGSYIKFD ENAAVIIKN DNDPRGTRIF GPVGRELREK KFMKIVSLAP EVL

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #16: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 15.602244 KDa
SequenceString:
MSVIKLHDLK PAPGEKKAKT RVGRGEGSKG KTAGRGTKGT KARKNVPVMF EGGQMPIHMR LPKLKGFKNR FRTEYQVVNV GDINKAFPQ GGTVGVDELV AKGLVRKNSL VKVLGDGKLT VKVDVTANKF SGSAREAITA AGGSATEL

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #17: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 15.77424 KDa
SequenceString:
MLIPRKVKHR KQHHPEQRGI ASGGTSVSFG DYGIQALEHA YITNRQIESA RIAINRHIKR GGKVWINIFP DRPLTKKPAE TRMGSGKGS PEWWVANVKP GRVLFELSYP DEKTARDALT RAIHKLPIKA RIVTREEQF

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #18: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 21.892246 KDa
SequenceString: MPKPTKGPRL GGSSSHQSAL LANLATSLFE HGRIKTTEPK ARALRPYAEK LITHAKKGAL HNRREVMKKI RDKDVVHTLF AEIGPFYAD RNGGYTRIIK VENRKGDNAP MAVIELVREK TVTDEANRAR RAAASQAKAD ERADEKADEK AEETVEETTE A PAEESTEA ...String:
MPKPTKGPRL GGSSSHQSAL LANLATSLFE HGRIKTTEPK ARALRPYAEK LITHAKKGAL HNRREVMKKI RDKDVVHTLF AEIGPFYAD RNGGYTRIIK VENRKGDNAP MAVIELVREK TVTDEANRAR RAAASQAKAD ERADEKADEK AEETVEETTE A PAEESTEA AAEETVEETT EAPAEESTEA AEESEAKDDT K

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #19: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.711728 KDa
SequenceString:
MAHKPVGQNI SEVRRNARLR RHARLRKKVA GTAEVPRLVV NRSARHIHVQ LVNDLNGTTL AAASSIEADV RAIDGDKKAH SVRVGQLIA ERAKAAGVET VVFDRGGYTY GGRIAALADA AREAGLKF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #20: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 12.892806 KDa
SequenceString:
MNTLDFVDQA SLRDDIPTFS PGDTVNVHVK VIEGSKERIQ VFKGVVIRRQ GGGISETFTV RKESYGVGVE RTFPVHSPNI DHIDVLTRG DVRRAKLYYL RELRGKKAKI KEKR

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #21: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 14.494693 KDa
SequenceString:
MARVKRALNA QKKRRTVLKA SKGYRGQRSR LYRKAKEQQL HSLTYAYRDR RARKGEFRKL WISRINAAAR ANDITYNRLI QGLKAAGVE VDRKNLAELA VSDPAAFTAL VDVARAALPE DVNAPSGEAA

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #22: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.055894 KDa
SequenceString:
MATYAIVKTG GKQYKVAAGD VVKVEKLDSE PGASVSLPVA LVVDGANVTS KADDLAKVAV TAEVLEHTKG PKIRIHKFKN KTGYHKRQG HRQQLTVLKV TGIK

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #23: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 16.3536 KDa
SequenceString:
MSTVTEFPSA TAKARYVRVS ATKARRVIDL VRGKSVEEAL DILRWAPQAA SEPVAKVIAS AAANAQNNEG LDPSTLVVAT VYADEGPTA KRIRPRAQGR AFRIRKRTSH ITVIVESRPP KQKGASAASA RSRRAQGSKA AATKKSAETK EGSE

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #24: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.047836 KDa
SequenceString:
MATITDPRDI ILAPVISEKS YGLIEDNVYT FVVHPDSNKT QIKIAIEKIF DVKVDSVNTA NRQGKRKRTR TGFGKRKSTK RAIVKLAAG SKPIDLFGAP A

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #25: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.228946 KDa
SequenceString:
MKVHKGDTVL VISGKDKGAK GKVLVAYPDR NKVLVEGVNR IKKHTAVSAN ERGASSGGIV TQEAPIHVSN VMVVDSDGKP TRVGYRIDD ETGKKVRIAK TNGKDI

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #26: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 22.571078 KDa
SequenceString: MAKTANIPNK LTANVRTRTG KGASRQARRD GKVPAVLYGH GTDPQHLELN ARDFAAVLRS HGTNAILTLD IEGTEQLALT KALDVHPIR RNIQHADLLV VQRGEKVTVE VTVLVEGDAT PGTLVTQDAN TIEIEAEALS IPEQLTVSVE GVEAGTQITA G QISLPEGV ...String:
MAKTANIPNK LTANVRTRTG KGASRQARRD GKVPAVLYGH GTDPQHLELN ARDFAAVLRS HGTNAILTLD IEGTEQLALT KALDVHPIR RNIQHADLLV VQRGEKVTVE VTVLVEGDAT PGTLVTQDAN TIEIEAEALS IPEQLTVSVE GVEAGTQITA G QISLPEGV NLISDPELLV VNVVEAPSAE ALEEEGAGET GAAEAPAEEA PAEEPAE

UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #27: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 9.249582 KDa
SequenceString:
MAHKKGASSS RNGRDSAAQR LGVKRFGGQV VKAGEILVRQ RGTHFHPGVN VGRGGDDTLF ALAPGAVEFG AKRGRKTVNI VPVARPEA

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #28: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 6.891016 KDa
SequenceString:
MAAVCDICGK GPGFGKSVSH SHRRTSRRWN PNIQPVRAVT RPGGNKQRIN ACTSCIKAGK VSRA

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #29: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 8.790895 KDa
SequenceString:
MAVGTTPGEL RELTDDELKD KLRESKEELF NLRFQMATGQ LSNNRRLRTV RQEIARVYTV LRERELGLAS GPAGEES

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #30: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 7.022147 KDa
SequenceString:
MAELKITQVR STIGARWKQR ESLRTLGLKK IRQSVVREDN AQTRGLINTV HHLVEVEEVG K

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #31: Uncharacterized protein bL37

MacromoleculeName: Uncharacterized protein bL37 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 2.841375 KDa
SequenceString:
MAKRGRKKRD RKHSKANHGK RPNA

UniProtKB: Uncharacterized protein

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Macromolecule #6: 23S RNA

MacromoleculeName: 23S RNA / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 1.0262834379999999 MDa
SequenceString: UUGUAAGUGU UUAAGGGCGC AUGGUGGAUG CCUUGGCACU GGGAGCCGAU GAAGGACGUA GGAGGCUGCG AUAAGCCUCG GGGAGCUGU CAACCGAGCG UUGAUCCGAG GAUGUCCGAA UGGGGAAACC CGGCACGAGU GAUGUCGUGU CACCAGGCGC U GAAUAUAU ...String:
UUGUAAGUGU UUAAGGGCGC AUGGUGGAUG CCUUGGCACU GGGAGCCGAU GAAGGACGUA GGAGGCUGCG AUAAGCCUCG GGGAGCUGU CAACCGAGCG UUGAUCCGAG GAUGUCCGAA UGGGGAAACC CGGCACGAGU GAUGUCGUGU CACCAGGCGC U GAAUAUAU AGGCGUCUGG GGGGAACGCG GGGAAGUGAA ACAUCUCAGU ACCCGUAGGA AGAGAAAACA AAAUGUGAUU CC GUGAGUA GUGGCGAGCG AAAGCGGAGG AUGGCUAAAC CGUAUGCAUG UGAUACCGGG UAGGGGUUGU GUGUGCGGGG UUG UGGGAC CUAUCUUUCC GGCUCUACCU GGCUGGAGGG CAGUGAGAAA AUGUUGUGGU UAGCGGAAAU GGCUUGGGAU GGCC UGCCG UAGACGGUGA GAGCCCGGUA CGUGAAAACC CGACGUCUGU CUUGAUGGUG UUCCCGAGUA GCAGCGGGCC CGUGG AAUC UGCUGUGAAU CUGCCGGGAC CACCCGGUAA GCCUGAAUAC UUCCCAGUGA CCGAUAGCGG AUUAGUACCG UGAGGG AAU GGUGAAAAGU ACCCCGGGAG GGGAGUGAAA GAGUACCUGA AACCGUGCGC UUACAAUCCG UCAGAGCCCU CGACGUG UC GUGGGGUGAU GGCGUGCCUU UUGAAGAAUG AGCCUGCGAG UCAGGGACAU GUCGCGAGGU UAACCCGGGU GGGGUAGC C GCAGCGAAAG CGAGUCUGAA UAGGGCGUAU CCACACAAGA GUGUGUGGUG UAGUGGUGUG UUCUGGACCC GAAGCGGAG UGAUCUACCC AUGGCCAGGG UGAAGCGCGG GUAAGACCGC GUGGAGGCCC GAACCCACUU AGGUUGAAGA CUGAGGGGAU GAGCUGUGG GUAGGGGUGA AAGGCCAAUC AAACUCCGUG AUAGCUGGUU CUCCCCGAAA UGCAUUUAGG UGCAGCGUCG C AUGUUUCU UGCCGGAGGU AGAGCUACUG GAUGGCCGAU GGGCCCCACA GGGUUACUGA CGUCAGCCAA ACUCCGAAUG CC GGUAAGU CCAAGAGUGC GGCAGUGGGA CGGCGGGGGA UAAGCUCCGU GCGUCGAGAG GGAAACAGCC CAGAUCGCCG GCU AAGGCC CCUAAGCGUG UGCUAAGUGG AAAAGGAUGU GCAGUCGCGA AGACAACCAG GAGGUUGGCU UAGAAGCAGC CACC CUUGA AAGAGUGCGU AAUAGCUCAC UGGUCAAGUG AUUGUGCGCC GAUAAUGUAG CGGGGCUCAA GCACACCGCC GAAGC CGCG GCAGCCAACG UGUUGGCUGG GUAGGGGAGC GUCCUGCAUC CGGUGAAGCC GCCGAGUGAU CGAGUGGUGG AGGGUG UGG GAGUGAGAAU GCAGGCAUGA GUAGCGAUUA GGCAAGUGAG AACCUUGCCC GCCGAAAGAC CAAGGGUUCC UGGGCCA GG CCAGUCCGCC CAGGGUGAGU CGGGACCUAA GGCGAGGCCG ACAGGCGUAG UCGAUGGACA ACGGGUUGAU AUUCCCGU A CCCGUGUAUG UGCGUCCAUG AUGAAUCAGC GGUACUAACC AUCCAAAACC ACCGUGACCG CACCUUUCGG GGUGUGGCG UUGGUGGGGC UGCAUGGGAC CUUCGUUGGU AGUAGUCAAG CGAUGGGGUG ACGCAGGAAG GUAGCCGUAC CGGUCAGUGG UAAUACCGG GGUAAGCCUG UAGGGAGUCA GAUAGGUAAA UCCGUCUGGC AUAUAUCCUG AGAGGUGAUG CAUAGCCGAG U GAGGCGAA UUCGGUGAUC CUAUGCUGCC GAGAAAAGCC UCUAGCGAGG ACAUACACGG CCCGUACCCC AAACCAACAC AG GUGGUCA GGUAGAGAAU ACUAAGGCGU ACGAGUGAAC UAUGGUUAAG GAACUCGGCA AAAUGCCCCC GUAACUUCGG GAG AAGGGG GACCCACAUG GCGUGUAAGC CUUUACGGCC CAAGCGUGAG UGGGUGGCAC AAACCAGUGA GAAGCGACUG UUUA CUAAA AACACAGGUC CGUGCGAAGU CGCAAGACGA UGUAUACGGA CUGACGCCUG CCCGGUGCUG GAAGGUUAAG AGGAC CCGU UAACUCCCUU UGGGGGUGAA GCGGAGAAUU UAAGCCCCAG UAAACGGCGG UGGUAACUAU AACCAUCCUA AGGUAG CGA AAUUCCUUGU CGGGUAAGUU CCGACCUGCA CGAAUGGCGU AACGACUUCU CAACUGUCUC AACCAUAGAC UCGGCGA AA UUGCACUACG AGUAAAGAUG CUCGUUACGC GCGGCAGGAC GAAAAGACCC CGGGACCUUC ACUACAACUU GGUAUUGG U GCUCGAUACG GUUUGUGUAG GAUAGGUGGG AGACUGUGAA GCUCACACGC CAGUGUGGGU GGAGUCGUUG UUGAAAUAC CACUCUGAUC GUAUUGGGCC UCUAACCUCG GACCGUAUAU CCGGUUCAGG GACAGUGCCU GGUGGGUAGU UUAACUGGGG CGGUUGCCU CCUAAAAUGU AACGGAGGCG CCCAAAGGUU CCCUCAACCU GGACGGCAAU CAGGUGUUGA GUGUAAGUGC A CAAGGGAG CUUGACUGCG AGACGGACAU GUCGAGCAGG GACGAAAGUC GGGACUAGUG AUCCGGCACC UCUGAGUGGA AG GGGUGUC GCUCAACGGA UAAAAGGUAC CCCGGGGAUA ACAGGCUGAU CUUCCCCAAG AGUCCAUAUC GACGGGAUGG UUU GGCACC UCGAUGUCGG CUCGUCGCAU CCUGGGGCUG GAGCAGGUCC CAAGGGUUGG GCUGUUCGCC CAUUAAAGCG GCAC GCGAG CUGGGUUUAG AACGUCGUGA GACAGUUCGG UCUCUAUCCG CCGCGCGCGU CAGAAGCUUG AGGAAACCUG UCCCU AGUA CGAGAGGACC GGGACGGACG AACCUCUGGU AUACCAGUUG UCCCACCAGG GGCACGGCUG GAUAGCCACG UUCGGA CAG GAUAACCGCU GAAAGCAUCU AAGCGGGAAA CCUCUUCCAA GACCAGGCUU CUCACCCUCU AGGAGGGAUA AGGCCCC CC GCAGACCACG GGAUUGAUAG ACCAGACCUG GAAGCCUAGU AAUAGGUGCA GGGAACUGGC ACUAACCGGC CGAAAACU U ACAACACCCC AUAAUCGUUG UAAGAAGAAA ACAUUGACGC ACC

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Macromolecule #7: 5S RNA

MacromoleculeName: 5S RNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 38.038777 KDa
SequenceString:
GUUACGGCGG UCCAUAGCGG CAGGGAAACG CCCGGUCCCA UCCCGAACCC GGAAGCUAAG CCUGCCAGCG CCGAUGAUAC UACCCUUCC GGGUGGAAAA GUAGGACACC GCCGAACAC

GENBANK: GENBANK: CP000480.1

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Macromolecule #32: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 32 / Number of copies: 146 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71351
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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