SAXSdb — 1mji

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

50S ribosomal protein L5

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 2 RNA 2	5S rRNA fragment × 2 MAGNESIUM ION × 4 POTASSIUM ION × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL5_THETH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–182； UniProt 1–182 Author chain B； PDBConstruct 1–182； UniProt 1–182

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	1mji
Deposition date deposition_date	2002-08-28
Structure title title	DETAILED ANALYSIS OF RNA-PROTEIN INTERACTIONS WITHIN THE BACTERIAL RIBOSOMAL PROTEIN L5/5S RRNA COMPLEX
Keywords keywords	ribosomal protein - 5S rRNA complex, RIBOSOME; 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.

1mji__assembly_1__model_1

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

Download this curve (.dat)

1mji__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mji__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.82 Å
Rg (electron density)	24.91 Å
Total Rg	25.49 Å
Atom count	4366
Residues	423
Excluded volume	73341 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mji__assembly_1__model_1`	tetrameric （4）	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	5S rRNA fragment
Molecular weight formula_weight	10847.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	4553

GGCACCUGACCCCAUGCCGAACUCAGAAGUGCCC

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562

Entity 2 Entity 2 polymer

Description description	50S ribosomal protein L5
Molecular weight formula_weight	21155.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFRK

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1mjia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.77 — RL5-like
Superfamily Superfamily superfamily	d.77.1 — RL5-like
Family Family family	d.77.1.1 — Ribosomal protein L5

Domain ID domain_id	d1mjib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.77 — RL5-like
Superfamily Superfamily superfamily	d.77.1 — RL5-like
Family Family family	d.77.1.1 — Ribosomal protein L5

CATH v4.4 (2 domains)

Domain ID domain_id	1mjiA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1440 — 50s Ribosomal Protein L5; Chain: A,
Homologous superfamily homologous superfamily	10 — Ribosomal protein L5

Domain ID domain_id	1mjiB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1440 — 50s Ribosomal Protein L5; Chain: A,
Homologous superfamily homologous superfamily	10 — Ribosomal protein L5

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Unit-cell length a length_a	51.890 Å
Unit-cell length b length_b	99.600 Å
Unit-cell length c length_c	65.730 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	14.910 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2880

DETAILED ANALYSIS OF RNA-PROTEIN INTERACTIONS WITHIN THE BACTERIAL RIBOSOMAL PROTEIN L5/5S RRNA COMPLEX

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

50S ribosomal protein L5

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

1mji__assembly_1__model_1

1mji__assembly_1__model_1 | I(q)

1mji__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

DETAILED ANALYSIS OF RNA-PROTEIN INTERACTIONS WITHIN THE BACTERIAL RIBOSOMAL PROTEIN L5/5S RRNA COMPLEX

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

50S ribosomal protein L5

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

1mji__assembly_1__model_1

1mji__assembly_1__model_1 | I(q)

1mji__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)