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

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Entry
Database: PDB / ID: 5xym
TitleLarge subunit of Mycobacterium smegmatis
DescriptorUncharacterized protein/RNA Complex
(50S ribosomal protein ...) x 28
KeywordsRIBOSOME / Mycobacterium smegmatis ribosome / rRNA / rprotein
Specimen sourceMycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
MethodElectron microscopy (3.08 Å resolution / Particle / Single particle)
AuthorsLi, Z. / Ge, X. / Zhang, Y. / Zheng, L. / Sanyal, S. / Gao, N.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jul 9, 2017 / Release: Sep 27, 2017

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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 01234CDEFG...

#1: Polypeptide(L)50S ribosomal protein L32 / bL32


Mass: 6467.719 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0R3I9

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)50S ribosomal protein L33 2 / bL33


Mass: 6615.640 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0R551

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)50S ribosomal protein L34 / bL34


Mass: 5522.580 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0R7K0

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)50S ribosomal protein L35 / bL35


Mass: 7298.505 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QYU7

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)50S ribosomal protein L36 / bL36


Mass: 4341.277 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSL4

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)50S ribosomal protein L2 / uL2


Mass: 30425.945 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSD4

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)50S ribosomal protein L3 / uL3


Mass: 23011.393 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSD1

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)50S ribosomal protein L4 / uL4


Mass: 22920.949 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSD2

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)50S ribosomal protein L5 / uL5


Mass: 21152.328 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSG1

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)50S ribosomal protein L6 / uL6


Mass: 19483.361 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSG4

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)50S ribosomal protein L9 / bL9


Mass: 15949.253 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0R7F6

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)50S ribosomal protein L13 / uL13


Mass: 16146.689 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSP8

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)50S ribosomal protein L14 / uL14


Mass: 13400.625 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSF9

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)50S ribosomal protein L15 / uL15


Mass: 15602.244 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: I7G436

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)50S ribosomal protein L16 / uL16


Mass: 15774.240 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSD8

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)50S ribosomal protein L17 / bL17


Mass: 21892.246 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSL9

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)50S ribosomal protein L18 / uL18


Mass: 13711.728 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: I7FGD9

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)50S ribosomal protein L19 / bL19


Mass: 12892.806 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QV42

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)50S ribosomal protein L20 / bL20


Mass: 14494.693 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QYU6

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)50S ribosomal protein L21 / bL21


Mass: 11055.894 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0R151

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)50S ribosomal protein L22 / uL22


Mass: 16353.600 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSD6

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)50S ribosomal protein L23 / uL23


Mass: 11047.836 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSD3

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S ribosomal protein L24 / uL24


Mass: 11228.946 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSG0

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S ribosomal protein L25 / bL25


Mass: 22571.078 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: I7GFB2

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein L27 / bL27


Mass: 9249.582 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0R150

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S ribosomal protein L28 / bL28


Mass: 6891.016 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: I7FJ52

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S ribosomal protein L29 / uL29


Mass: 8790.895 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSD9

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S ribosomal protein L30 / uL30


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

Cellular component

Molecular function

Biological process

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RNA chain , 2 types, 2 molecules AB

#6: RNA chain23S RNA


Mass: 1026283.438 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
#7: RNA chain5S RNA


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

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Polypeptide(L) / Non-polymers , 2 types, 147 molecules a

#31: Polypeptide(L)Uncharacterized protein bL37


Mass: 2841.375 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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)
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 FIELD
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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