24YW | pdb_000024yw

Xanthomonas citri pv. glycines 50S subunit

PDB DOI: https://doi.org/10.2210/pdb24YW/pdb
EM Map EMD-69918: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Xanthomonas citri pv. glycines
Mutation(s): No

Deposited: 2026-03-25 Released: 2026-08-26
Deposition Author(s): Sengupta, S., Anand, R.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of 50S ribosomal subunit from phytopathogen Xanthomonas citri pv. glycines

Sengupta, S., Tripathy, J., Bandyopadhay, N., Gautam, S., Anand, R.

(2026) ACS Omega

Macromolecule Content

Total Structure Weight: 1,330.97 kDa
Atom Count: 86,233
Modeled Residue Count: 5,975
Deposited Residue Count: 6,257
Unique protein chains: 27
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL32	A [auth 2]	64	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL33	B [auth 3]	55	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL34	C [auth 4]	46	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL35	D [auth 5]	65	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL36	E [auth 6]	41	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL2	H [auth C]	275	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL3	I [auth D]	216	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	J [auth E]	201	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL6	K [auth G]	175	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL9	L [auth H]	149	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13	M [auth J]	142	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL14	N [auth K]	122	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL15	O [auth L]	147	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL16	P [auth M]	137	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL17	Q [auth N]	127	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL18	R [auth O]	119	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL19	S [auth P]	135	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL20	T [auth Q]	119	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL21	U [auth R]	106	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL22	V [auth S]	111	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	W [auth T]	99	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL24	X [auth U]	105	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL25	Y [auth V]	211	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL27	Z [auth W]	86	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL28	AA [auth X]	78	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL29	BA [auth Y]	61	Xanthomonas citri pv. glycines	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL30	CA [auth Z]	63	Xanthomonas citri pv. glycines	Mutation(s): 0
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
RNA (2797-MER)	F [auth A]	2,881	Xanthomonas citri pv. glycines
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
RNA (117-MER)	G [auth B]	121	Xanthomonas citri pv. glycines
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Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	RELION	4.0.1

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Sengupta, S.

Anand, R.

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	--

Revision History (Full details and data files)

Version 1.0: 2026-08-26
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

24YW | pdb_000024yw

Xanthomonas citri pv. glycines 50S subunit

Literature

Structure of 50S ribosomal subunit from phytopathogen Xanthomonas citri pv. glycines

Biological Assembly 1

Macromolecules

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