SAXSdb — 9ykj

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

Helicase ATP-binding domain-containing protein

Sinorhizobium meliloti

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q92XN4_RHIME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–845； UniProt 1–845 Author chain B； PDBConstruct 1–845； UniProt 1–845

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	9ykj
Deposition date deposition_date	2025-10-07
Structure title title	Hna Dimer
Keywords keywords	PD(D/E)XK nuclease, Superfamily 2 helicase, Anti-bacteriophage protein, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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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.

9ykj__assembly_1__model_1

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

Download this curve (.dat)

9ykj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ykj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.86 Å
Rg (electron density)	40.57 Å
Total Rg	40.70 Å
Atom count	5952
Residues	1205
Excluded volume	96186 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ykj__assembly_1__model_1`	dimeric （2）	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 (1)

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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	—

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

Resolution resolution	4.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	183538

Description description	Helicase ATP-binding domain-containing protein
Molecular weight formula_weight	94841.2 kDa
Source method src_method	man
Copy count entity_count	2

Hna Dimer

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

Helicase ATP-binding domain-containing protein

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

9ykj__assembly_1__model_1

9ykj__assembly_1__model_1 | I(q)

9ykj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5952

Source organism organism	Sinorhizobium meliloti
NCBI taxonomy ID ncbi_taxonomy_id	382
Host organism host_organism	Escherichia coli

Hna Dimer

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

Helicase ATP-binding domain-containing protein

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

9ykj__assembly_1__model_1

9ykj__assembly_1__model_1 | I(q)

9ykj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)