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9ufz

Ubiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii

Method: ELECTRON MICROSCOPY D_max: 103.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ufz
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

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	32.41 Å
rg_electron	31.03 Å
i0	253087000.00
molecular_weight	145150.0 kDa
excluded_volume	188460 Å³
envelope_volume	212010 Å³
shell_volume	53539 Å³
envelope_diameter	107.6 Å
shell_rg	40.48 Å
envelope_rg	31.50 Å
shape_rg	31.04 Å
total_rg	31.79 Å
total_atoms	10254
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

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3. P(r) Analysis (GNOM)

dmax	103.6 Å
rg_real	32.23 Å
rg_real_error	0.54 Å
i0_real	2.5310e+08
i0_real_error	3.7830e+06
rg_reciprocal	32.31 Å
i0_reciprocal	253100000.0000
total_estimate	0.8952
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.2 Å
skewness	0.196
kurtosis	-0.455
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0001
highest_alpha	64250000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.954

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4. Crystallography & Experiment

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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	10264

IFGKLGWDSIPTEPIVLVTMVFMALGAIAVLGGITYFKKWGYLWKEWFTTVDHKKIGIMYIIVSVVMLLRGFADAIMMRLQLFLAKGGGEGYLHPDHYDQIFTAHGVIMIFFVAMGLVVGMMNISVPLQIGARDVAFPLLNSLSFWLFAGAAGLMMLSLVLGEFAATGWMAYPPLSGIQYSPGVGVDYYIWALQVSGLGTLLSGVNFFVTIIKMRAPGMKLMDMPIFTWTSLCTAVLIIASFPVLTGTLAMLTLDRYFGFHFFTNELGGSPMLYVNLIWTWGHPEVYILVLPAFGLYSEIVATFSRKALFGYKSMVYATIAITVLAFVVWLHHFFTMGAGANVNAFFGIMTMVIAIPTGVKIFSWLFTMYKGRITFTTPMLWTLGFLVTFGIGGLTGVLMAVPPADFLVHNSLFLIAHFHNVIIGGVVFGMFAGIIYYWPKMFGWKLNEAWGKAAFWFWFFGFYFAFMPLYILGFLGMTRRLNTYDNPEWDPYLAIALFGAVLVAIGIACFLMQIIVGFLQRHQNMDYTGDPWDARTLEWATSSPAPFYNFAHEPDASGIDRFWTDKENGVAYARNTKYEDIHMPTDRAAGFVIAMFITLLGFALIWHIWWLVVVSFVAAVVSLIVSSFTKNVDYYVPAAEVERIENERYALLEKHLKKD

Source

organism	Acinetobacter baumannii
ncbi_taxonomy_id	470
host_organism	Escherichia coli

Entity 2 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 3 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 4 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 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	3

Entity 10 non-polymer

description	Ubiquinone-8
formula_weight	727.1 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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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	3.280 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.28 Å
resolution_method	—
num_particles	48128

fit	/app/data/saxs_computation/uf/9ufz/9ufz.fit
pddf	/app/data/pr_computation/uf/9ufz/9ufz.pr.out
profile	/app/data/saxs_computation/uf/9ufz/9ufz.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)