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9rzv

E. coli cytochrome bd-I dimer bound to menaquinone

Method: ELECTRON MICROSCOPY D_max: 136.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rzv
deposition_date	2025-07-16
title	E. coli cytochrome bd-I dimer bound to menaquinone
keywords	Oxireductase, Complex, Quinone, Substrate, membrane protein, Escherichia coli, 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	41.19 Å
rg_electron	40.26 Å
i0	587715000.00
molecular_weight	229970.0 kDa
excluded_volume	299610 Å³
envelope_volume	350250 Å³
shell_volume	70121 Å³
envelope_diameter	138.9 Å
shell_rg	47.50 Å
envelope_rg	40.00 Å
shape_rg	40.25 Å
total_rg	40.69 Å
total_atoms	32830
n_residues	1902
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	136.8 Å
rg_real	41.12 Å
rg_real_error	1.07 Å
i0_real	5.8770e+08
i0_real_error	1.0300e+07
rg_reciprocal	41.19 Å
i0_reciprocal	587800000.0000
total_estimate	0.8890
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	50.4 Å
skewness	0.259
kurtosis	-0.431
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	108200000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.903

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4. Crystallography & Experiment

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5. Entities & Polymer Info (13)

Entity 1 polymer

description	Cytochrome bd-I ubiquinol oxidase subunit 1
formula_weight	58251.7 kDa
ec_number	7.1.1.7
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,a
atom_count	32907

MLDIVELSRLQFALTAMYHFLFVPLTLGMAFLLAIMETVYVLSGKQIYKDMTKFWGKLFGINFALGVATGLTMEFQFGTNWSYYSHYVGDIFGAPLAIEGLMAFFLESTFVGLFFFGWDRLGKVQHMCVTWLVALGSNLSALWILVANGWMQNPIASDFNFETMRMEMVSFSELVLNPVAQVKFVHTVASGYVTGAMFILGISAWYMLKGRDFAFAKRSFAIAASFGMAAVLSVIVLGDESGYEMGDVQKTKLAAIEAEWETQPAPAAFTLFGIPDQEEETNKFAIQIPYALGIIATRSVDTPVIGLKELMVQHEERIRNGMKAYSLLEQLRSGSTDQAVRDQFNSMKKDLGYGLLLKRYTPNVADATEAQIQQATKDSIPRVAPLYFAFRIMVACGFLLLAIIALSFWSVIRNRIGEKKWLLRAALYGIPLPWIAVEAGWFVAEYGRQPWAIGEVLPTAVANSSLTAGDLIFSMVLICGLYTLFLVAELFLMFKFARLGPSSLKTGRYHFEQSSTTTQPAR

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 2 polymer

description	Cytochrome bd-I ubiquinol oxidase subunit 2
formula_weight	42479.8 kDa
ec_number	7.1.1.7
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,b

MIDYEVLRFIWWLLVGVLLIGFAVTDGFDMGVGMLTRFLGRNDTERRIMINSIAPHWDGNQVWLITAGGALFAAWPMVYAAAFSGFYVAMILVLASLFFRPVGFDYRSKIEETRWRNMWDWGIFIGSFVPPLVIGVAFGNLLQGVPFNVDEYLRLYYTGNFFQLLNPFGLLAGVVSVGMIITQGATYLQMRTVGELHLRTRATAQVAALVTLVCFALAGVWVMYGIDGYVVKSTMDHYAASNPLNKEVVREAGAWLVNFNNTPILWAIPALGVVLPLLTILTARMDKAAWAFVFSSLTLACIILTAGIAMFPFVMPSSTMMNASLTMWDATSSQLTLNVMTWVAVVLVPIILLYTAWCYWKMFGRITKEDIERNTHSLY

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 3 polymer

description	Cytochrome bd-I ubiquinol oxidase CydH (Uncharacterized protein YnhF)
formula_weight	2999.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,h

MSTDLKFSLVTTIIVLGLIVAVGLTAALH

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 4 polymer

description	Cytochrome bd-I ubiquinol oxidase subunit X
formula_weight	4043.7 kDa
ec_number	7.1.1.7
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	X,x

MWYFAWILGTLLACSFGVITALALEHVESGKAGQEDI

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 5 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	TRANS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
formula_weight	636.5 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	MENAQUINONE-9
formula_weight	785.2 kDa
src_method	syn
entity_count	4

Entity 8 non-polymer

description	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
formula_weight	648.9 kDa
src_method	syn
entity_count	6

Entity 9 non-polymer

description	Ubiquinone-8
formula_weight	727.1 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	OXYGEN MOLECULE
formula_weight	32.0 kDa
src_method	syn
entity_count	2

Entity 11 non-polymer

description	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
formula_weight	751.0 kDa
src_method	nat
entity_count	4

Entity 12 non-polymer

description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
formula_weight	760.1 kDa
src_method	syn
entity_count	4

Entity 13 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	77

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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	2.23 Å
resolution_method	—
num_particles	530094

fit	/app/data/saxs_computation/rz/9rzv/9rzv.fit
pddf	/app/data/pr_computation/rz/9rzv/9rzv.pr.out
profile	/app/data/saxs_computation/rz/9rzv/9rzv.dat

E. coli cytochrome bd-I dimer bound to menaquinone

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 (13)

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

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)