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- PDB-5xyu: Small subunit of Mycobacterium smegmatis ribosome -

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Entry
Database: PDB / ID: 5xyu
TitleSmall subunit of Mycobacterium smegmatis ribosome
DescriptorConserved domain protein/RNA Complex
(30S ribosomal protein ...) x 18
KeywordsRIBOSOME / Mycobacterium smegmatis ribosome / rRNA / rprotein
Specimen sourceMycobacterium smegmatis (strain atcc 700084 / mc(2)155) / bacteria
MethodElectron microscopy (3.45 Å resolution / Particle / Single particle)
AuthorsLi, Z. / Zhang, Y. / Zheng, L. / Ge, X. / 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 10, 2017 / Release: Sep 27, 2017

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Assembly

Deposited unit
A: 16S RNA
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18 2
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)764,82568
Polyers763,65920
Non-polymers1,16748
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)84890
ΔGint (kcal/M)-1114
Surface area (Å2)262500

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Components

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30S ribosomal protein ... , 18 types, 18 molecules CDEFGHIJKL...

#2: Polypeptide(L)30S ribosomal protein S3 / uS3


Mass: 30191.227 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSD7
#3: Polypeptide(L)30S ribosomal protein S4 / uS4


Mass: 23415.787 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSL7
#4: Polypeptide(L)30S ribosomal protein S5 / uS5


Mass: 21946.090 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSG6
#5: Polypeptide(L)30S ribosomal protein S6 / bS6


Mass: 10200.688 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0R7F9
#6: Polypeptide(L)30S ribosomal protein S7 / uS7


Mass: 17660.375 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QS97
#7: Polypeptide(L)30S ribosomal protein S8 / uS8


Mass: 14492.638 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSG3
#8: Polypeptide(L)30S ribosomal protein S9 / uS9


Mass: 16794.365 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSP9
#9: Polypeptide(L)30S ribosomal protein S10 / uS10


Mass: 11454.313 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSD0
#10: Polypeptide(L)30S ribosomal protein S11 / uS11


Mass: 14671.762 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSL6
#11: Polypeptide(L)30S ribosomal protein S12 / uS12


Mass: 13896.366 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QS96
#12: Polypeptide(L)30S ribosomal protein S13 / uS13


Mass: 14249.619 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSL5
#13: Polypeptide(L)30S ribosomal protein S14 type Z / uS14


Mass: 6976.409 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSG2
#14: Polypeptide(L)30S ribosomal protein S15 / uS15


Mass: 10368.097 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QVQ3
#15: Polypeptide(L)30S ribosomal protein S16 / bS16


Mass: 16795.207 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QV37
#16: Polypeptide(L)30S ribosomal protein S17 / uS17


Mass: 11127.002 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSE0
#17: Polypeptide(L)30S ribosomal protein S18 2 / bS18


Mass: 9524.188 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0R7F7
#18: Polypeptide(L)30S ribosomal protein S19 / uS19


Mass: 10800.602 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QSD5
#19: Polypeptide(L)30S ribosomal protein S20 / bS20


Mass: 9556.104 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0R102

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RNA chain / Polypeptide(L) / Non-polymers , 3 types, 50 molecules AU

#1: RNA chain16S RNA


Mass: 495373.656 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: GenBank: 118168627
#20: Polypeptide(L)Conserved domain protein / uL41


Mass: 4164.300 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
References: UniProt: A0QR10
#21: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 48 / 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: Small 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
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: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 47338 / Symmetry type: POINT

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