1j3l

Structure of the RNA-processing inhibitor RraA from Thermus thermophilis

Method: X-RAY DIFFRACTION

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

Demethylmenaquinone Methyltransferase

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	MAGNESIUM ION × 1 CHLORIDE ION × 2 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P83846_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–164； UniProt 1–164 Author chain B； PDBConstruct 1–164； UniProt 1–164 Author chain C； PDBConstruct 1–164； UniProt 1–164 Author chain D； PDBConstruct 1–164； UniProt 1–164 Author chain E； PDBConstruct 1–164； UniProt 1–164 Author chain F； PDBConstruct 1–164； UniProt 1–164

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	1j3l
Deposition date deposition_date	2003-02-04
Structure title title	Structure of the RNA-processing inhibitor RraA from Thermus thermophilis
Keywords keywords	Vitamine K2, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

1j3l__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1j3l__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1j3l__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.01 Å
Rg (electron density)	23.87 Å
Total Rg	24.70 Å
Atom count	3633
Residues	482
Excluded volume	65095 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1j3l__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1j3l__assembly_2__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	Demethylmenaquinone Methyltransferase
Molecular weight formula_weight	17456.8 kDa
EC 编号 ec_number	2.1.1.-
Mutation mutation	L80R
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7692

MEARTTDLSDLYPEGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPSGVRSGG

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	398

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1j3la_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

Domain ID domain_id	d1j3lb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

Domain ID domain_id	d1j3lc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

Domain ID domain_id	d1j3ld_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

Domain ID domain_id	d1j3le_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

Domain ID domain_id	d1j3lf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

CATH v4.4 (6 domains)

Domain ID domain_id	1j3lA00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

Domain ID domain_id	1j3lB00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

Domain ID domain_id	1j3lC00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

Domain ID domain_id	1j3lD00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

Domain ID domain_id	1j3lE00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

Domain ID domain_id	1j3lF00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

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Unit-cell length a length_a	61.872 Å
Unit-cell length b length_b	109.068 Å
Unit-cell length c length_c	270.319 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	38.400 Å
R factor r_factor	0.2100
R_work r_work	0.2060
R_free r_free	0.2740

Structure of the RNA-processing inhibitor RraA from Thermus thermophilis

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

Demethylmenaquinone Methyltransferase

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

1j3l__assembly_2__model_1

1j3l__assembly_2__model_1 | I(q)

1j3l__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of the RNA-processing inhibitor RraA from Thermus thermophilis

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

Demethylmenaquinone Methyltransferase

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

1j3l__assembly_2__model_1

1j3l__assembly_2__model_1 | I(q)

1j3l__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)