SAXSdb — 2o9l

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

RNA polymerase sigma factor RpoN

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPTPTPTPGPGPCPAPCPGPTPTPTPC)-3' × 1 5'-D(GPAPAPAPCPGPTPGPCPCPAPAPAPA)-3' × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O66858_AQUAE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 3–63； UniProt 338–398

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	2o9l
Deposition date deposition_date	2006-12-13
Structure title title	AMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element
Keywords keywords	;AMBER, GENERALIZED BORN SOLVENT MODEL, PROTEIN-DNA COMPLEX, HELIX-TURN-HELIX, TRANSCRIPTION FACTOR, SIGMA-54, RNA POLYMERASE, RNA POLYMERASE SIGMA FACTOR RPON-DNA COMPLEX ;; RNA POLYMERASE SIGMA FACTOR RPON/DNA
Experimental Method method	SOLUTION NMR

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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.

2o9l__assembly_1__model_3

Assembly 1 · Model 3 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2o9l__assembly_1__model_3 | I(q)

100 plotted points; both axes use logarithmic scales.

2o9l__assembly_1__model_3 | P(r) · Pending

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

Rg（Guinier）	16.62 Å
Rg (electron density)	15.73 Å
Total Rg	16.62 Å
Atom count	1861
Residues	91
Excluded volume	17736 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2o9l__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2o9l__assembly_1__model_2`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2o9l__assembly_1__model_3`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2o9l__assembly_1__model_4`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2o9l__assembly_1__model_5`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2o9l__assembly_1__model_6`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2o9l__assembly_1__model_7`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2o9l__assembly_1__model_8`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2o9l__assembly_1__model_9`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2o9l__assembly_1__model_10`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`2o9l__assembly_1__model_11`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`2o9l__assembly_1__model_12`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`2o9l__assembly_1__model_13`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`2o9l__assembly_1__model_14`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`2o9l__assembly_1__model_15`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`2o9l__assembly_1__model_16`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	17	`2o9l__assembly_1__model_17`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	18	`2o9l__assembly_1__model_18`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	19	`2o9l__assembly_1__model_19`	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 (3)

Entity 1 Entity 1 polymer

Description description	5'-D(TPTPTPTPGPGPCPAPCPGPTPTPTPC)-3'
Molecular weight formula_weight	4252.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	35359

TTTTGGCACGTTTC

Entity 2 Entity 2 polymer

Description description	5'-D(GPAPAPAPCPGPTPGPCPCPAPAPAPA)-3'
Molecular weight formula_weight	4306.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GAAACGTGCCAAAA

Entity 3 Entity 3 polymer

Description description	RNA polymerase sigma factor RpoN
Molecular weight formula_weight	7488.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

HMLTQGELMKLIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERRI

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2o9lA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

AMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element

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

RNA polymerase sigma factor RpoN

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

2o9l__assembly_1__model_3

2o9l__assembly_1__model_3 | I(q)

2o9l__assembly_1__model_3 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

AMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element

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

RNA polymerase sigma factor RpoN

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

2o9l__assembly_1__model_3

2o9l__assembly_1__model_3 | I(q)

2o9l__assembly_1__model_3 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)