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9ufb

Ubiquinol Binding Site of Cytochrome bo3 from A.b

Method: ELECTRON MICROSCOPY D_max: 101.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ufb
deposition_date	2025-04-10
title	Ubiquinol Binding Site of Cytochrome bo3 from A.b
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	32.42 Å
rg_electron	31.03 Å
i0	252683000.00
molecular_weight	144420.0 kDa
excluded_volume	187270 Å³
envelope_volume	210380 Å³
shell_volume	53204 Å³
envelope_diameter	110.0 Å
shell_rg	40.39 Å
envelope_rg	31.50 Å
shape_rg	31.04 Å
total_rg	31.76 Å
total_atoms	10200
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	101.0 Å
rg_real	32.25 Å
rg_real_error	0.66 Å
i0_real	2.5270e+08
i0_real_error	3.7810e+06
rg_reciprocal	32.32 Å
i0_reciprocal	252700000.0000
total_estimate	0.8969
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.2 Å
skewness	0.203
kurtosis	-0.447
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	65990000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.887

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

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	10210

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	1,2-Distearoyl-sn-glycerophosphoethanolamine
formula_weight	748.1 kDa
src_method	syn
entity_count	8

Entity 6 non-polymer

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

Entity 7 non-polymer

description	HEME O
formula_weight	838.9 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

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

Entity 9 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	3.050 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.05 Å
resolution_method	—
num_particles	196159

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

Ubiquinol Binding Site of Cytochrome bo3 from A.b

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 (9)

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

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)