SAXSdb — 9vdt

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

Ion transport protein

Aliarcobacter butzleri (strain RM4018)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SODIUM ION × 8 CHAPSO × 4 DODECYL-BETA-D-MALTOSIDE × 4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8EVM5_ALIB4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–269； UniProt 1–267

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	9vdt
Deposition date deposition_date	2025-06-09
Structure title title	Crystal structure of voltage-gated sodium channel NavAb N49K DC230 mutant
Keywords keywords	ion channel, MEMBRANE PROTEIN; MEMBRANE 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.

9vdt__assembly_1__model_1

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

Download this curve (.dat)

9vdt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vdt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.31 Å
Rg (electron density)	32.65 Å
Total Rg	33.42 Å
Atom count	8874
Residues	868
Excluded volume	172310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vdt__assembly_1__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	Ion transport protein
Molecular weight formula_weight	31253.1 kDa
Mutation mutation	N49K
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2225

GSMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFKQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTSLKN

Source Source

Source organism organism	Aliarcobacter butzleri (strain RM4018)
NCBI taxonomy ID ncbi_taxonomy_id	367737
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHAPSO
Molecular weight formula_weight	631.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	678.9 kDa
Source method src_method	nat
Copy count entity_count	8

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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Unit-cell length a length_a	129.755 Å
Unit-cell length b length_b	129.755 Å
Unit-cell length c length_c	200.315 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	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	tetragonal

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	29.690 Å
R factor r_factor	0.3099
R_work r_work	0.3084
R_free r_free	0.3444

Crystal structure of voltage-gated sodium channel NavAb N49K DC230 mutant

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

Ion transport 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

9vdt__assembly_1__model_1

9vdt__assembly_1__model_1 | I(q)

9vdt__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of voltage-gated sodium channel NavAb N49K DC230 mutant

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

Ion transport 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

9vdt__assembly_1__model_1

9vdt__assembly_1__model_1 | I(q)

9vdt__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)