SAXSdb — 1y69

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

50S ribosomal protein L16

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 2	23S ribosomal RNA × 1 5S ribosomal RNA × 1 50S ribosomal protein L27 × 1 （Q9RY65） Ribosome-recycling factor × 1 （P0A805）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL16_DEIRA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain K； PDBConstruct 1–141； UniProt 1–141

50S ribosomal protein L27

OrganismNot specified

UniProt Q9RY65

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 2	23S ribosomal RNA × 1 5S ribosomal RNA × 1 50S ribosomal protein L16 × 1 （Q9RXJ5） Ribosome-recycling factor × 1 （P0A805）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL27_DEIRA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain U； PDBConstruct 1–91； UniProt 1–91

Ribosome-recycling factor

Escherichia coli

UniProt P0A805

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 2	23S ribosomal RNA × 1 5S ribosomal RNA × 1 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L27 × 1 （Q9RY65）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRF_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain 8； PDBConstruct 1–30； UniProt 1–30 Author chain 8； PDBConstruct 34–113； UniProt 106–185

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	1y69
Deposition date deposition_date	2004-12-04
Structure title title	RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans
Keywords keywords	RIBOSOME, 50S, RRF, RECYCLING FACTOR; 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.

1y69__assembly_1__model_1

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

Download this curve (.dat)

1y69__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y69__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	66.60 Å
Rg (electron density)	66.15 Å
Total Rg	66.27 Å
Atom count	64484
Residues	3217
Excluded volume	919080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y69__assembly_1__model_1`	pentameric （5）	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 (5)

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	64484

GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAUCAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCCCUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAACCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUACCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUGCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUGGUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGAUAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCACCCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUGAGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC

Entity 2 Entity 2 polymer

Description description	5S ribosomal RNA
Molecular weight formula_weight	39911.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	9

ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUUU

Entity 3 Entity 3 polymer

Description description	50S ribosomal protein L16
Molecular weight formula_weight	16126.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTKMVKREVYDEAQ

Entity 4 Entity 4 polymer

Description description	50S ribosomal protein L27
Molecular weight formula_weight	9609.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

MAHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAAQTEVAAD

Entity 5 Entity 5 polymer

Description description	Ribosome-recycling factor
Molecular weight formula_weight	12844.6 kDa
Mutation mutation	RRF domain II deletion and GGG insertion
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	8

MISDIRKDAEVRMDKCVEAFKTQISKIRTGGGGTEERRKDLTKIVRGEAEQARVAVRNVRRDANDKVKALLKDKEISEDDDRRSQDDVQKLTDAAIKKIEAALADKEAELMQF

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1y69k1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.4 — Ribosomal protein L16p/L10e
Family Family family	d.41.4.2 — Ribosomal protein L16p

Domain ID domain_id	d1y69u1
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.4 — Ribosomal L27 protein-like
Family Family family	b.84.4.1 — Ribosomal L27 protein

CATH v4.4 (3 domains)

Domain ID domain_id	1y69800
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily	20 — Ribosome-recycling factor

Domain ID domain_id	1y69K01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	10 — Ribosomal protein L16/L10

Domain ID domain_id	1y69U01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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Unit-cell length a length_a	168.700 Å
Unit-cell length b length_b	405.000 Å
Unit-cell length c length_c	693.000 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	3.330 Å
Low-resolution limit resolution_low	8.130 Å
R factor r_factor	0.2750
R_work r_work	0.2750
R_free r_free	0.3380

RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans

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

50S ribosomal protein L16

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L27

State in the Current Structure

Other States of the Same Protein in the Database

Ribosome-recycling factor

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

1y69__assembly_1__model_1

1y69__assembly_1__model_1 | I(q)

1y69__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans

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

50S ribosomal protein L16

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S ribosomal protein L27

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribosome-recycling factor

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

1y69__assembly_1__model_1

1y69__assembly_1__model_1 | I(q)

1y69__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)