SAXSdb — 2ogm

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1. Protein Identity and Related Structures Protein Identity & Related Structures

50S ribosomal protein L3

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	23S ribosomal RNA × 1 ;(2S,3AR,4R,5S,6S,8R,9R,9AR,10R)-2,5-DIHYDROXY-4,6,9,10-TETRAMETHYL-1-OXO-6-VINYLDECAHYDRO-3A,9-PROP[1]ENOCYCLOPENTA[8]ANNULEN-8-YL [(6-AMINOPYRIDAZIN-3-YL)CARBONYL]CARBAMATE ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL3_DEIRA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–211； UniProt 1–211

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ogm
Deposition date deposition_date	2007-01-07
Structure title title	The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519
Keywords keywords	SB-571519, pleuromutilin, PTC, peptidyl transferase center, ribosome, antibiotic; RIBOSOME
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2ogm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ogm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ogm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	65.72 Å
Rg (electron density)	65.35 Å
Total Rg	65.67 Å
Atom count	59406
Residues	2767
Excluded volume	864650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ogm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	23S ribosomal RNA
Molecular weight formula_weight	933405.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	0
Atom count atom_count	59610

GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAUCAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCCCUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAACCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUACCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUGCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUGGUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGAUAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCACCCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUGAGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC

Entity 2 Entity 2 polymer

Description description	50S ribosomal protein L3
Molecular weight formula_weight	22477.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRSAAKASAAKGGK

Entity 3 Entity 3 non-polymer

Description description	;(2S,3AR,4R,5S,6S,8R,9R,9AR,10R)-2,5-DIHYDROXY-4,6,9,10-TETRAMETHYL-1-OXO-6-VINYLDECAHYDRO-3A,9-PROP[1]ENOCYCLOPENTA[8]ANNULEN-8-YL [(6-AMINOPYRIDAZIN-3-YL)CARBONYL]CARBAMATE ;
Molecular weight formula_weight	498.6 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2ogmb1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.2 — Ribosomal protein L3

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Unit-cell length a length_a	170.396 Å
Unit-cell length b length_b	405.835 Å
Unit-cell length c length_c	703.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	29.930 Å
R factor r_factor	—
R_work r_work	0.2750
R_free r_free	0.3340

The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519

1. Protein Identity and Related Structures Protein Identity & Related Structures

50S ribosomal protein L3

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ogm__assembly_1__model_1

2ogm__assembly_1__model_1 | I(q)

2ogm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)

The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519

1. Protein Identity and Related Structures Protein Identity & Related Structures

50S ribosomal protein L3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ogm__assembly_1__model_1

2ogm__assembly_1__model_1 | I(q)

2ogm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)