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- PDB-5xym: Large subunit of Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 5xym
TitleLarge subunit of Mycobacterium smegmatis
Components
  • (50S ribosomal protein ...) x 28
  • 23S RNA
  • 5S RNA5S ribosomal RNA
  • Uncharacterized protein bL37
KeywordsRIBOSOME / Mycobacterium smegmatis ribosome / rRNA / rprotein
Function / homologyRibosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L25, C-terminal / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L19 superfamily ...Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L25, C-terminal / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L19 superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L14 superfamily / Ribosomal protein L20 signature. / Ribosomal protein L6 / Ribosomal protein L5, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, N-terminal / Ribosomal protein L22/L17 superfamily / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L30p/L7e / Ribosomal protein L36 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L6 signature 1. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L15 signature. / Ribosomal protein L29 signature. / Ribosomal protein L9, C-terminal domain / Ribosomal protein L33 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L30 signature. / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L34 signature. / Ribosomal protein L36 signature. / Ribosomal protein TL5, C-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L20 / Ribosomal prokaryotic L21 protein / KOW motif / Ribosomal protein L34 / Ribosomal protein L33 / Ribosomal protein L13 / Ribosomal protein L4/L1 family / ribosomal L5P family C-terminus / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L28 family / Ribosomal L32p protein family / Ribosomal L29 protein / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L27 protein / Ribosomal protein L17 / Ribosomal protein L19 / Ribosomal protein L9, N-terminal domain / Ribosomal L25p family / Ribosomal protein L35 / Ribosomal protein L2, C-terminal / Ribosomal protein L35 / Ribosomal protein L35 signature. / Ribosomal protein L32p / Ribosomal protein L21 / Ribosomal protein L29/L35 / Ribosomal protein L19 / Ribosomal protein L5 / Ribosomal protein L4/L1e / Ribosomal protein L2 / Ribosomal protein L6, conserved site / Ribosomal protein L24 / Ribosomal protein L33 / Ribosomal protein L18, bacterial-type / Ribosomal protein L18 / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L13 / Ribosomal protein L35, non-mitochondrial
Function and homology information
Specimen sourceMycobacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.08 Å resolution
AuthorsLi, Z. / Ge, X. / Zhang, Y. / Zheng, L. / Sanyal, S. / Gao, N.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 9, 2017 / Release: Sep 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 27, 2017Structure modelrepositoryInitial release
1.1Apr 11, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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Assembly

Deposited unit
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33 2
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
A: 23S RNA
B: 5S RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
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
a: Uncharacterized protein bL37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,462,027177
Polyers1,458,47931
Non-polymers3,549146
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)171740
ΔGint (kcal/M)-2657
Surface area (Å2)456670

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Components

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50S ribosomal protein ... , 28 types, 28 molecules 01234CDEFGHJKLMNOPQRSTUVWXYZ

#1: Protein/peptide 50S ribosomal protein L32 / / bL32


Mass: 6467.719 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R3I9
#2: Protein/peptide 50S ribosomal protein L33 2 / Ribosome / bL33


Mass: 6615.640 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R551
#3: Protein/peptide 50S ribosomal protein L34 / / bL34


Mass: 5522.580 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R7K0
#4: Protein/peptide 50S ribosomal protein L35 / / bL35


Mass: 7298.505 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QYU7
#5: Protein/peptide 50S ribosomal protein L36 / / bL36


Mass: 4341.277 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL4
#8: Protein/peptide 50S ribosomal protein L2 / / uL2


Mass: 30425.945 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD4
#9: Protein/peptide 50S ribosomal protein L3 / / uL3


Mass: 23011.393 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD1
#10: Protein/peptide 50S ribosomal protein L4 / / uL4


Mass: 22920.949 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD2
#11: Protein/peptide 50S ribosomal protein L5 / / uL5


Mass: 21152.328 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG1
#12: Protein/peptide 50S ribosomal protein L6 / / uL6


Mass: 19483.361 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG4
#13: Protein/peptide 50S ribosomal protein L9 / / bL9


Mass: 15949.253 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R7F6
#14: Protein/peptide 50S ribosomal protein L13 / / uL13


Mass: 16146.689 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSP8
#15: Protein/peptide 50S ribosomal protein L14 / / uL14


Mass: 13400.625 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSF9
#16: Protein/peptide 50S ribosomal protein L15 / / uL15


Mass: 15602.244 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7G436, UniProt: A0QSG8*PLUS
#17: Protein/peptide 50S ribosomal protein L16 / / uL16


Mass: 15774.240 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD8
#18: Protein/peptide 50S ribosomal protein L17 / / bL17


Mass: 21892.246 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL9
#19: Protein/peptide 50S ribosomal protein L18 / / uL18


Mass: 13711.728 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7FGD9, UniProt: A0QSG5*PLUS
#20: Protein/peptide 50S ribosomal protein L19 / / bL19


Mass: 12892.806 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QV42
#21: Protein/peptide 50S ribosomal protein L20 / / bL20


Mass: 14494.693 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QYU6
#22: Protein/peptide 50S ribosomal protein L21 / / bL21


Mass: 11055.894 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R151
#23: Protein/peptide 50S ribosomal protein L22 / / uL22


Mass: 16353.600 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD6
#24: Protein/peptide 50S ribosomal protein L23 / / uL23


Mass: 11047.836 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD3
#25: Protein/peptide 50S ribosomal protein L24 / / uL24


Mass: 11228.946 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG0
#26: Protein/peptide 50S ribosomal protein L25 / / bL25


Mass: 22571.078 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7GFB2, UniProt: A0R3D2*PLUS
#27: Protein/peptide 50S ribosomal protein L27 / / bL27


Mass: 9249.582 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R150
#28: Protein/peptide 50S ribosomal protein L28 / / bL28


Mass: 6891.016 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7FJ52, UniProt: A0QV03*PLUS
#29: Protein/peptide 50S ribosomal protein L29 / / uL29


Mass: 8790.895 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD9
#30: Protein/peptide 50S ribosomal protein L30 / / uL30


Mass: 7022.147 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG7

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RNA chain , 2 types, 2 molecules AB

#6: RNA chain 23S RNA


Mass: 1026283.438 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
#7: RNA chain 5S RNA / 5S ribosomal RNA


Mass: 38038.777 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627

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Protein/peptide / Non-polymers , 2 types, 147 molecules a

#31: Protein/peptide Uncharacterized protein bL37


Mass: 2841.375 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QTP4
#32: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 146 / Formula: Mg / Magnesium

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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: Large subunit of Mycobacterium smegmatis ribosome / 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
Source: NATURAL
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 71351 / Symmetry type: POINT

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