SAXSdb — 4jc0

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

Ribosomal protein S12 methylthiotransferase RimO

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	IRON/SULFUR PENTA-SULFIDE CONNECTED CLUSTERS × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	IRON/SULFUR PENTA-SULFIDE CONNECTED CLUSTERS × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIMO_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–430； UniProt 1–430 Author chain B； PDBConstruct 1–430； UniProt 1–430

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	4jc0
Deposition date deposition_date	2013-02-20
Structure title title	Crystal structure of Thermotoga maritima holo RimO in complex with pentasulfide, Northeast Structural Genomics Consortium Target VR77
Keywords keywords	;Structural Genomics, PSI-Biology, Northeast Structural Genomics Consortium, NESG, three-domained enzyme, alpha-beta N-terminal domain, Semi-TIM barrel Radical-SAM domain, beta barrel C-terminal TRAM domain, ribosomal protein S12, TRANSFERASE ;; TRANSFERASE
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.

4jc0__assembly_1__model_1

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

Download this curve (.dat)

4jc0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4jc0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.95 Å
Rg (electron density)	22.03 Å
Total Rg	22.63 Å
Atom count	3440
Residues	424
Excluded volume	61743 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jc0__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4jc0__assembly_2__model_1`	monomeric （1）	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 (2)

Entity 1 Entity 1 polymer

Description description	Ribosomal protein S12 methylthiotransferase RimO
Molecular weight formula_weight	50360.4 kDa
EC 编号 ec_number	2.-.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6850

MRVGIKVLGCPKNEADCEVLAGVLREGGHEIVFDVKDADVVVLDTCAFIEDAKRESIDEIFSFVDAKDQYGYKLVVKGCLVQRYYEELKKEIPEVDQWIGVADPEEIANAIENGTDLVPDQPETVYRYRKRIDLEERPYAYVKISDGCDRGCTFCSIPSFKGSLRSRSIEDITREVEDLLKEGKKEIILVAQDTTSYGIDLYRKQALPDLLRRLNSLNGEFWIRVMYLHPDHLTEEIISAMLELDKVVKYFDVPVQHGSDKILKLMGRTKSSEELKKMLSSIRERFPDAVLRTSIIVGFPGETEEDFEELKQFVEEIQFDKLGAFVYSDEEGTVAFNLKEKVDPEMAKRRQEELLLLQAEISNSRLDRFVGKKLKFLVEGKEGKFLVGRTWTEAPEVDGVVFVRGKGKIGDFLEVVIKEHDEYDMWGSVILEHHHHHH

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR PENTA-SULFIDE CONNECTED CLUSTERS
Molecular weight formula_weight	863.6 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4jc0A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12160 — Methylthiotransferase, N-terminal domain

Domain ID domain_id	4jc0A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	4jc0A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4jc0A04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	4jc0B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12160 — Methylthiotransferase, N-terminal domain

Domain ID domain_id	4jc0B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	4jc0B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4jc0B04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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Unit-cell length a length_a	59.721 Å
Unit-cell length b length_b	86.948 Å
Unit-cell length c length_c	172.795 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	41.460 Å
R factor r_factor	0.2450
R_work r_work	0.2450
R_free r_free	0.2960

Crystal structure of Thermotoga maritima holo RimO in complex with pentasulfide, Northeast Structural Genomics Consortium Target VR77

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

Ribosomal protein S12 methylthiotransferase RimO

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

4jc0__assembly_1__model_1

4jc0__assembly_1__model_1 | I(q)

4jc0__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of Thermotoga maritima holo RimO in complex with pentasulfide, Northeast Structural Genomics Consortium Target VR77

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

Ribosomal protein S12 methylthiotransferase RimO

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

4jc0__assembly_1__model_1

4jc0__assembly_1__model_1 | I(q)

4jc0__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)