SAXSdb — 3a1p

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

Ribosome maturation factor rimM

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	30S ribosomal protein S19 × 1 （Q5SHP2） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	30S ribosomal protein S19 × 1 （Q5SHP2） UNKNOWN ATOM OR ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIMM_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 1–162 Author chain C； PDBConstruct 1–162； UniProt 1–162

30S ribosomal protein S19

Thermus thermophilus

UniProt Q5SHP2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ribosome maturation factor rimM × 1 （Q5SJH5） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ribosome maturation factor rimM × 1 （Q5SJH5） UNKNOWN ATOM OR ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS19_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–93； UniProt 1–93 Author chain D； PDBConstruct 1–93； UniProt 1–93

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	3a1p
Deposition date deposition_date	2009-04-21
Structure title title	Structure of Ribosome maturation protein RimM and Ribosomal protein S19
Keywords keywords	;RimM N-terminal domain, PRC-barrel domain, beta barrels, ribosome, 30S ribosomal subunit, ribosome biogenesis, 16S rRNA processing, ribosomal protein, rRNA binding, protein-protein complex, Chaperone, Cytoplasm, Ribonucleoprotein, RNA-binding, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; RIBOSOMAL PROTEIN
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.

3a1p__assembly_1__model_1

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

Download this curve (.dat)

3a1p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a1p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.19 Å
Rg (electron density)	21.43 Å
Total Rg	22.22 Å
Atom count	1955
Residues	246
Excluded volume	34999 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a1p__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3a1p__assembly_2__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ribosome maturation factor rimM
Molecular weight formula_weight	18094.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4317

MRLVEIGRFGAPYALKGGLRFRGEPVVLHLERVYVEGHGWRAIEDLYRVGEELVVHLAGVTDRTLAEALVGLRVYAEVADLPPLEEGRYYYFALIGLPVYVEGRQVGEVVDILDAGAQDVLIIRGVGERLRDRAERLVPLQAPYVRVEEGSIHVDPIPGLFD

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	30S ribosomal protein S19
Molecular weight formula_weight	10605.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MPRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	406

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3a1pA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	60 — RimM

Domain ID domain_id	3a1pA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	240 — PRC-barrel domain

Domain ID domain_id	3a1pB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	860 — 30s Ribosomal Protein S19; Chain A
Homologous superfamily homologous superfamily	10 — Ribosomal protein S19/S15

Domain ID domain_id	3a1pC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	60 — RimM

Domain ID domain_id	3a1pC02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	240 — PRC-barrel domain

Domain ID domain_id	3a1pD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	860 — 30s Ribosomal Protein S19; Chain A
Homologous superfamily homologous superfamily	10 — Ribosomal protein S19/S15

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Unit-cell length a length_a	57.397 Å
Unit-cell length b length_b	67.491 Å
Unit-cell length c length_c	62.002 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.82 °
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	2.300 Å
Low-resolution limit resolution_low	45.570 Å
R factor r_factor	—
R_work r_work	0.1970
R_free r_free	0.2450

Structure of Ribosome maturation protein RimM and Ribosomal protein S19

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

Ribosome maturation factor rimM

State in the Current Structure

Other States of the Same Protein in the Database

30S ribosomal protein S19

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

3a1p__assembly_1__model_1

3a1p__assembly_1__model_1 | I(q)

3a1p__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structure of Ribosome maturation protein RimM and Ribosomal protein S19

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

Ribosome maturation factor rimM

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S19

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

3a1p__assembly_1__model_1

3a1p__assembly_1__model_1 | I(q)

3a1p__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)