SAXSdb — 9v5h

▼

1. Structure Basics

entry_id	9v5h
deposition_date	2025-05-26
title	cryo-EM structure of hexameric ArnA
keywords	;Lipid A modification Polymyxin resistance Bifunctional enzyme UDP-glucuronic acid dehydrogenase UDP-4-amino-4-deoxy-L-arabinose, transferase Lipopolysaccharide biosynthesis Antibiotic resistance Aminotransferase Dehydrogenase LPS modification pathway L-Ara4N biosynthesis, TRANSFERASE ;; TRANSFERASE
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	52.24 Å
rg_electron	51.61 Å
i0	2413220000.00
molecular_weight	417770.0 kDa
excluded_volume	525480 Å³
envelope_volume	841080 Å³
shell_volume	129540 Å³
envelope_diameter	166.8 Å
shell_rg	60.39 Å
envelope_rg	49.80 Å
shape_rg	51.58 Å
total_rg	52.00 Å
total_atoms	29508
n_residues	3726
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	159.5 Å
rg_real	51.96 Å
rg_real_error	0.84 Å
i0_real	2.4130e+09
i0_real_error	4.5820e+07
rg_reciprocal	52.45 Å
i0_reciprocal	2415000000.0000
total_estimate	0.8249
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	63.8 Å
skewness	0.095
kurtosis	-0.563
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0001
highest_alpha	392800000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	Bifunctional polymyxin resistance protein ArnA
formula_weight	32717.4 kDa
ec_number	2.1.2.13,1.1.1.305
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	29508

MKTVVFAYHDMGCLGIEALLAAGYEISAIFTHTDNPGEKAFYGSVARLAAERGIPVYAPDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDEILQLAPAGAFNLHGSLLPKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQLRIAIAPDDIAITLHHKLCHAARQLLEQTLPAIKHGNILEIAQRENEATCFGRRTPDDSFLEWHKPASVLHNMVRAVADPWPGAFSYVGNQKFTVWSSRVHPHASKAQPGSVISVAPLLIACGDGALEIVTGQAGDGITMQGSQLAQTLGLVQ

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Bifunctional polymyxin resistance protein ArnA
formula_weight	39744.2 kDa
ec_number	2.1.2.13,1.1.1.305
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	G,H,I,J,K,L

MRVLILGVNGFIGNHLTERLLREDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVAIATPIEYTRNPLRVFELDFEENLRIIRYCVKYRKRIIFPSTSEVYGMCSDKYFDEDHSNLIVGPVNKPRWIYSVSKQLLDRVIWAYGEKEGLQFTLFRPFNWMGPRLDNLNAARIGSSRAITQLILNLVEGSPIKLIDGGKQKRCFTDIRDGIEALYRIIENAGNRCDGEIINIGNPENEASIEELGEMLLASFEKHPLRHHFPPFAGFRVVESSSYYGKGYQDVEHRKPSIRNAHRCLDWEPKIDMQETIDETLDFFLRTVDLTD

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

▶

6. Citations (2)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	4.00 Å
resolution_method	—
num_particles	74212

fit	/app/data/saxs_computation/v5/9v5h/9v5h.fit
pddf	/app/data/pr_computation/v5/9v5h/9v5h.pr.out
profile	/app/data/saxs_computation/v5/9v5h/9v5h.dat

cryo-EM structure of hexameric ArnA

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)