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- PDB-5o5j: Structure of the 30S small ribosomal subunit from Mycobacterium s... -

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Entry
Database: PDB / ID: 5o5j
TitleStructure of the 30S small ribosomal subunit from Mycobacterium smegmatis
DescriptorConserved domain protein
50S ribosomal protein L31/RNA Complex
(30S ribosomal protein ...) x 19
KeywordsRIBOSOME / ribosome / translation
Specimen sourceMycobacterium smegmatis str. mc2 155 / bacteria
MethodElectron microscopy (3.45 Å resolution / Particle / Single particle)
AuthorsHentschel, J. / Burnside, C. / Mignot, I. / Leibundgut, M. / Boehringer, D. / Ban, N.
CitationCell Rep, 2017, 20, 149-160

Cell Rep, 2017, 20, 149-160 Yorodumi Papers
The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Jendrik Hentschel / Chloe Burnside / Ingrid Mignot / Marc Leibundgut / Daniel Boehringer / Nenad Ban

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 2, 2017 / Release: Jul 12, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 12, 2017Structure modelrepositoryInitial release
1.1Jul 19, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Assembly

Deposited unit
A: 16S rRNA
B: Conserved domain protein
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
V: 30S ribosomal protein S2
W: tRNA-Phe anticodon stem
X: mRNA fragment
g: 50S ribosomal protein L31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)816,244243
Polyers810,83924
Non-polymers5,405219
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)114790
ΔGint (kcal/M)-2579
Surface area (Å2)287600
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules AWX

#1: RNA chain16S rRNA


Mass: 495373.656 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: GenBank: 118168627
#22: RNA chaintRNA-Phe anticodon stem


Mass: 6140.736 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155
#23: RNA chainmRNA fragment


Mass: 1791.053 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155

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Polypeptide(L) , 2 types, 2 molecules Bg

#2: Polypeptide(L)Conserved domain protein / bS22 / 30S ribosomal protein bS22


Mass: 4164.300 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QR10
#24: Polypeptide(L)50S ribosomal protein L31 / bL31


Mass: 8312.485 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0R215

Cellular component

Molecular function

Biological process

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30S ribosomal protein ... , 19 types, 19 molecules CDEFGHIJKL...

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


Mass: 30191.227 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSD7

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)30S ribosomal protein S4 / uS4


Mass: 23415.787 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSL7

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)30S ribosomal protein S5 / uS5


Mass: 21946.090 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSG6

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)30S ribosomal protein S6 / bS6


Mass: 10991.637 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0A0D6J3X3

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)30S ribosomal protein S7 / uS7


Mass: 17660.375 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QS97

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)30S ribosomal protein S8 / uS8


Mass: 14492.638 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSG3

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)30S ribosomal protein S9 / uS9


Mass: 16794.365 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSP9

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)30S ribosomal protein S10 / uS10


Mass: 11454.313 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSD0

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)30S ribosomal protein S11 / uS11


Mass: 14671.762 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSL6

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)30S ribosomal protein S12 / uS12


Mass: 13896.366 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QS96

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)30S ribosomal protein S13 / uS13


Mass: 14249.619 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSL5

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)30S ribosomal protein S14 type Z / uS14


Mass: 6976.409 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSG2

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)30S ribosomal protein S15 / uS15


Mass: 10368.097 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QVQ3

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)30S ribosomal protein S16 / bS16


Mass: 16795.207 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QV37

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)30S ribosomal protein S17 / uS17


Mass: 11127.002 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSE0

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)30S ribosomal protein S18 2 / bS18


Mass: 9524.188 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0R7F7

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)30S ribosomal protein S19 / uS19


Mass: 10800.602 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QSD5

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)30S ribosomal protein S20 / bS20


Mass: 9556.104 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0R102

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)30S ribosomal protein S2 / uS2


Mass: 30145.230 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis str. MC2 155 / References: UniProt: A0QVB8

Cellular component

Molecular function

Biological process

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Non-polymers , 2 types, 219 molecules

#25: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 217 / Formula: Mg
#26: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn

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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: 30S small ribosomal subunit / 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
Source: NATURAL
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE / Humidity: 96 %

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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 / Calibrated magnification: 100719
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Details: FEI EPU data collection / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 7

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDFitting ID
1EMAN Boxer1.9PARTICLE SELECTION1
4CTFFIND3CTF CORRECTION1
9RELION1.4INITIAL EULER ASSIGNMENT1
10RELION1.4FINAL EULER ASSIGNMENT1
12RELION1.4RECONSTRUCTION1
19PHENIXMODEL REFINEMENT1
CTF correctionDetails: CTF correction in Relion / Type: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 224584 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER
Refine
Refine IDR factor R freeR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection R freeNumber reflection obsPercent reflection R freePercent reflection obsOverall SU MLSigma FOverall phase errorSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
10.24180.23050.23083.45149.3593447713781112.5099.960.450.9825.380.901.11MLHLFLAT BULK SOLVENT MODEL
ELECTRON MICROSCOPY
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00856171
ELECTRON MICROSCOPYf_angle_d1.13283477
ELECTRON MICROSCOPYf_dihedral_angle_d17.46625957
ELECTRON MICROSCOPYf_chiral_restr0.04810576
ELECTRON MICROSCOPYf_plane_restr0.0064881
Refine LS shell

Refine ID: ELECTRON MICROSCOPY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.45100.50500.48733.4902117145113100.00
3.49020.40650.37023.5313114644889100.00
3.53130.36320.34543.5743114844700100.00
3.57430.34080.33333.6196111644974100.00
3.61960.34760.32293.6672114044320100.00
3.66720.31750.31223.7174112044893100.00
3.71740.31180.30583.7705117245358100.00
3.77050.29980.29193.8268103644190100.00
3.82680.30260.28493.8865120045022100.00
3.88650.28050.27753.9502114444920100.00
3.95020.28180.26894.0183117644520100.00
4.01830.27500.26334.0913117144742100.00
4.09130.27980.25264.1700117945310100.00
4.17000.25960.24184.2551119244555100.00
4.25510.25120.23484.3475113144542100.00
4.34750.24720.22624.4486111844342100.00
4.44860.22910.22384.5598116145230100.00
4.55980.24020.21624.6830111944757100.00
4.68300.22500.20644.8207111544876100.00
4.82070.21490.20314.9761118344991100.00
4.97610.21030.19375.1538118944868100.00
5.15380.20330.19125.3599108444778100.00
5.35990.19380.18225.6035113444519100.00
5.60350.20050.17735.8985109045135100.00
5.89850.17900.17306.2674115044635100.00
6.26740.18560.17556.7502116344802100.00
6.75020.17790.16257.4274112044794100.00
7.42740.15320.15268.4975122545050100.00
8.49750.14920.143810.6880116544432100.00
10.68800.15060.149749.364212194437799.00

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