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9wym

CryoEM structure of native quinol dependent Nitric Oxide Reductase with HQN at pH 6.5

Method: ELECTRON MICROSCOPY D_max: 112.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wym
deposition_date	2025-09-27
title	CryoEM structure of native quinol dependent Nitric Oxide Reductase with HQN at pH 6.5
keywords	quinol-dependent Nitric Oxide Reductase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	35.80 Å
rg_electron	34.86 Å
i0	353867000.00
molecular_weight	164420.0 kDa
excluded_volume	210090 Å³
envelope_volume	254540 Å³
shell_volume	58331 Å³
envelope_diameter	114.7 Å
shell_rg	43.39 Å
envelope_rg	34.87 Å
shape_rg	34.85 Å
total_rg	35.45 Å
total_atoms	11651
n_residues	1433
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	112.9 Å
rg_real	35.67 Å
rg_real_error	0.81 Å
i0_real	3.5390e+08
i0_real_error	5.4780e+06
rg_reciprocal	35.75 Å
i0_reciprocal	353900000.0000
total_estimate	0.8313
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.1 Å
skewness	0.181
kurtosis	-0.592
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	133500000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Nitric oxide reductase subunit B
formula_weight	84724.9 kDa
ec_number	1.7.2.5
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	12181

MGPYRRLWFTLIAVLAVTFALLGFYGGEVYRQAPPIPEEVASADGTRLFGRDDILDGQTAWQSIGGMQLGSIWGHGAYQAPDWTADWLHRELMAWLDLAARDAHGRDYGQLDAPAQAALREQLKAEYRANRADAAGGKLTLSPRRAQAVAQTEAYYDQLFSDAPALHRSRENYAMKENTLPDANRRRQMTHFFFWTAWAAATEREGTSVTYTNNWPHEPLIGNHPSSENVMWSIISVVVLLAGIGLLIWAWAFLRGKEEDEPPAPARDPLTTFALTPSQRALGKYLFLVVALFGFQVLLGGFTAHYTVEGQKFYGIDLSQWFPYSLVRTWHIQSALFWIATGFLAAGLFLAPLINGGRDPKYQKAGVDILFWALVLVVVGSFAGNYLAIAQIMPPDLNFWLGHQGYEYVDLGRLWQIGKFAGICFWLVLMLRGIVPALRTPGGDKNLLALLTASVGAIGLFYGAGFFYGERTHLTVMEYWRWWIVHLWVEGFFEVFATTALAFIFSTLGLVSRRMATTASLASASLFMLGGIPGTFHHLYFAGTTTPVMAVGASFSALEVVPLIVLGHEAWENWRLKTRAPWMENLKWPLMCFVAVAFWNMLGAGVFGFMINPPVSLYYIQGLNTTPVHAHAALFGVYGFLALGFTLLVLRYIRPQYALSPGLMKLAFWGLNLGLALMIFTSLLPIGLIQFHASVSEGMWYARSEAFMQQDILKTLRWGRTFGDVVFLLGALAMVVQVILGLLSGKPAAAEPVLRAEPARR

Source

organism	Achromobacter xylosoxidans
ncbi_taxonomy_id	85698
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

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

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	nat
entity_count	2

Entity 5 non-polymer

description	DODECYL-BETA-D-MALTOSIDE
formula_weight	510.6 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	benzene-1,2,4-triol
formula_weight	126.1 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
formula_weight	522.8 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	506

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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	2.300 Å
resolution_low	2.300 Å
r_factor	0.3412
r_work	0.3412
r_free	—

resolution	2.30 Å
resolution_method	—
num_particles	767273

fit	/app/data/saxs_computation/wy/9wym/9wym.fit
pddf	/app/data/pr_computation/wy/9wym/9wym.pr.out
profile	/app/data/saxs_computation/wy/9wym/9wym.dat