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- PDB-24yw: Xanthomonas citri pv. glycines 50S subunit -

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Basic information

Entry
Database: PDB / ID: 24yw
TitleXanthomonas citri pv. glycines 50S subunit
Components
  • (Large ribosomal subunit protein ...) x 27
  • RNA (117-MER)
  • RNA (2797-MER)
KeywordsRIBOSOME / Phytopathogen / Xanthomonas citri pv. glycines / 50S subunit
Function / homology
Function and homology information


: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / : / : / : ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / :
Similarity search - Component
Biological speciesXanthomonas citri pv. glycines (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsSengupta, S. / Anand, R.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
CitationJournal: Acs Omega / Year: 2026
Title: Structure of 50S ribosomal subunit from phytopathogen Xanthomonas citri pv. glycines
Authors: Sengupta, S. / Tripathy, J. / Bandyopadhay, N. / Gautam, S. / Anand, R.
History
DepositionMar 25, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: Large ribosomal subunit protein bL32
3: Large ribosomal subunit protein bL33
4: Large ribosomal subunit protein bL34
5: Large ribosomal subunit protein bL35
6: Large ribosomal subunit protein bL36
A: RNA (2797-MER)
B: RNA (117-MER)
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
G: Large ribosomal subunit protein uL6
H: Large ribosomal subunit protein bL9
J: Large ribosomal subunit protein uL13
K: Large ribosomal subunit protein uL14
L: Large ribosomal subunit protein uL15
M: Large ribosomal subunit protein uL16
N: Large ribosomal subunit protein bL17
O: Large ribosomal subunit protein uL18
P: Large ribosomal subunit protein bL19
Q: Large ribosomal subunit protein bL20
R: Large ribosomal subunit protein bL21
S: Large ribosomal subunit protein uL22
T: Large ribosomal subunit protein uL23
U: Large ribosomal subunit protein uL24
V: Large ribosomal subunit protein bL25
W: Large ribosomal subunit protein bL27
X: Large ribosomal subunit protein bL28
Y: Large ribosomal subunit protein uL29
Z: Large ribosomal subunit protein uL30


Theoretical massNumber of molelcules
Total (without water)1,330,97229
Polymers1,330,97229
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Large ribosomal subunit protein ... , 27 types, 27 molecules 23456CDEGHJKLMNOPQRSTUVWXYZ

#1: Protein Large ribosomal subunit protein bL32


Mass: 7146.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HTU4
#2: Protein Large ribosomal subunit protein bL33


Mass: 6422.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HWN5
#3: Protein/peptide Large ribosomal subunit protein bL34


Mass: 5327.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HWA1
#4: Protein Large ribosomal subunit protein bL35


Mass: 7583.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0I0L4
#5: Protein/peptide Large ribosomal subunit protein bL36


Mass: 4887.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0I1I4
#8: Protein Large ribosomal subunit protein uL2


Mass: 29961.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HUI0
#9: Protein Large ribosomal subunit protein uL3


Mass: 22907.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HUK4
#10: Protein Large ribosomal subunit protein uL4


Mass: 21803.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HUR7
#11: Protein Large ribosomal subunit protein uL6


Mass: 18304.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HUH5
#12: Protein Large ribosomal subunit protein bL9


Mass: 15716.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0I4I2
#13: Protein Large ribosomal subunit protein uL13


Mass: 16110.677 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HVE2
#14: Protein Large ribosomal subunit protein uL14


Mass: 13547.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HU63
#15: Protein Large ribosomal subunit protein uL15


Mass: 15364.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HTY3
#16: Protein Large ribosomal subunit protein uL16


Mass: 15529.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HUF6
#17: Protein Large ribosomal subunit protein bL17


Mass: 14345.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HU83
#18: Protein Large ribosomal subunit protein uL18


Mass: 12827.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HUQ7
#19: Protein Large ribosomal subunit protein bL19


Mass: 14780.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HU77
#20: Protein Large ribosomal subunit protein bL20


Mass: 13385.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0I0J6
#21: Protein Large ribosomal subunit protein bL21


Mass: 11823.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HU45
#22: Protein Large ribosomal subunit protein uL22


Mass: 12098.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HU92
#23: Protein Large ribosomal subunit protein uL23


Mass: 11062.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HUB3
#24: Protein Large ribosomal subunit protein uL24


Mass: 11246.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HUK9
#25: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 23381.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HVG2
#26: Protein Large ribosomal subunit protein bL27


Mass: 9119.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HUH8
#27: Protein Large ribosomal subunit protein bL28


Mass: 9112.517 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HWI5
#28: Protein Large ribosomal subunit protein uL29


Mass: 7255.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HU43
#29: Protein Large ribosomal subunit protein uL30


Mass: 7223.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: UniProt: A0AAX0HUJ8

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RNA chain , 2 types, 2 molecules AB

#6: RNA chain RNA (2797-MER)


Mass: 933660.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: GenBank: 2021456405
#7: RNA chain RNA (117-MER)


Mass: 39033.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xanthomonas citri pv. glycines (bacteria) / References: GenBank: 1709611089

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 50S rebosomal subunit of Xanthomonas citri pv. glycine
Type: RIBOSOME / Entity ID: #6, #26, #2-#5, #8-#25, #27-#29, #7, #1 / Source: NATURAL
Source (natural)Organism: Xanthomonas citri pv. glycines (bacteria)
Buffer solutionpH: 7.5
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
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
1RELION4.0.1particle selection
2EPUimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9PHENIX1.21.1_5286model refinement
13RELION4.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252876 / Symmetry type: POINT

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