← Back to search

9ufw

Ubiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii

Method: ELECTRON MICROSCOPY D_max: 103.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9ufw
deposition_date	2025-04-10
title	Ubiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii
keywords	protein pump, ubiquinol, oxidase, OXIDOREDUCTASE; OXIDOREDUCTASE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.38 Å
rg_electron	30.99 Å
i0	251848000.00
molecular_weight	144840.0 kDa
excluded_volume	188100 Å³
envelope_volume	211080 Å³
shell_volume	53382 Å³
envelope_diameter	106.9 Å
shell_rg	40.41 Å
envelope_rg	31.47 Å
shape_rg	31.00 Å
total_rg	31.73 Å
total_atoms	10233
n_residues	1225
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	103.5 Å
rg_real	32.21 Å
rg_real_error	0.66 Å
i0_real	2.5180e+08
i0_real_error	3.8420e+06
rg_reciprocal	32.28 Å
i0_reciprocal	251900000.0000
total_estimate	0.6831
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	40.1 Å
skewness	0.202
kurtosis	-0.441
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	65870000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 0.999; Sysdev: 0.096; Positv: 1.000; Valcen: 0.992; Smooth: 0.912

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (10)

Entity 1 polymer

description	Cytochrome bo(3) ubiquinol oxidase subunit 1
formula_weight	74200.3 kDa
ec_number	7.1.1.3
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10243

IFGKLGWDSIPTEPIVLVTMVFMALGAIAVLGGITYFKKWGYLWKEWFTTVDHKKIGIMYIIVSVVMLLRGFADAIMMRLQLFLAKGGGEGYLHPDHYDQIFTAHGVIMIFFVAMGLVVGMMNISVPLQIGARDVAFPLLNSLSFWLFAGAAGLMMLSLVLGEFAATGWMAYPPLSGIQYSPGVGVDYYIWALQVSGLGTLLSGVNFFVTIIKMRAPGMKLMDMPIFTWTSLCTAVLIIASFPVLTGTLAMLTLDRYFGFHFFTNELGGSPMLYVNLIWTWGHPEVYILVLPAFGLYSEIVATFSRKALFGYKSMVYATIAITVLAFVVWLHHFFTMGAGANVNAFFGIMTMVIAIPTGVKIFSWLFTMYKGRITFTTPMLWTLGFLVTFGIGGLTGVLMAVPPADFLVHNSLFLIAHFHNVIIGGVVFGMFAGIIYYWPKMFGWKLNEAWGKAAFWFWFFGFYFAFMPLYILGFLGMTRRLNTYDNPEWDPYLAIALFGAVLVAIGIACFLMQIIVGFLQRHQNMDYTGDPWDARTLEWATSSPAPFYNFAHEPDASGIDRFWTDKENGVAYARNTKYEDIHMPTDRAAGFVIAMFITLLGFALIWHIWWLVVVSFVAAVVSLIVSSFTKNVDYYVPAAEVERIENERYALLEKHLKKD

Source

organism	Acinetobacter baumannii
ncbi_taxonomy_id	470
host_organism	Escherichia coli

Entity 2 polymer

description	Cytochrome bo(3) ubiquinol oxidase subunit 3
formula_weight	21569.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

HEHDDTDLTVFGFWTYLMSDLILFGSLFIAFAVLSSHVPPGTPSAYDLFHESLGYVLTETFALLISSVTFGFAVLASYKKNVNQVITWLFITFLFGATFIGMELYEFHHLVEEGHGPTHSAFLSSFFTLVGTHGIHVTSGLVWMLVLMYQIKTKGLTLPNTRRLACLSLFWHFLDIVWICVFSVVYLLGVL

Source

organism	Acinetobacter baumannii
ncbi_taxonomy_id	470
host_organism	Escherichia coli

Entity 3 polymer

description	Cytochrome bo(3) ubiquinol oxidase subunit 4
formula_weight	10882.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

GSVKTYMTGFILSIILTVIPFGMVMAGGFSRGLLVTVIAITAVAQVLVQLVYFLHMNTSSEQRWNMIAFIYTILCIAVLLIGSVWIMNYLHYNMMIH

Source

organism	Acinetobacter baumannii
ncbi_taxonomy_id	470
host_organism	Escherichia coli

Entity 4 polymer

description	Ubiquinol oxidase subunit 2
formula_weight	31121.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GDMVLLNSKGPVGQGQSDLMMTAIYLMLLVVIPSIIMALWFGWKYRASNKDADYKPTWAHSTAIEVVVWGIPVIIIGILAWLTWWGSHKYDPYRPLESDKAPLTIQVIAEQFKWIFIYPEQNIATVNEVRFPEKTPLSFKITSNFTMNSFFIPQLGGQIYAMAGMQTHLHLLANETGVYRGFSSNYSGYGFSQMRFKAHSVTEQQFNEWVAAVKAGNGTTINPEAVQKTTLDQAELATLRDGDRSKHQIEHLVNRAKAAGDQEALAKAEAMKPFPTK

Source

organism	Acinetobacter baumannii
ncbi_taxonomy_id	470
host_organism	Escherichia coli

Entity 5 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	HEME O
formula_weight	838.9 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	1,2-Distearoyl-sn-glycerophosphoethanolamine
formula_weight	748.1 kDa
src_method	syn
entity_count	6

Entity 9 non-polymer

description	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
formula_weight	787.2 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	Ubiquinone-8
formula_weight	727.1 kDa
src_method	syn
entity_count	1

▶

6. Citations (1)

▶

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	3.120 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.12 Å
resolution_method	—
num_particles	49809

fit	/app/data/saxs_computation/uf/9ufw/9ufw.fit
pddf	/app/data/pr_computation/uf/9ufw/9ufw.pr.out
profile	/app/data/saxs_computation/uf/9ufw/9ufw.dat

Ubiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii

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

Refinement

EM 3D

5. Entities & Polymer Info (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)