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9wyl

CryoEM structure of quinol dependent Nitric Oxide Reductase with BRIL

Method: ELECTRON MICROSCOPY D_max: 143.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wyl
deposition_date	2025-09-27
title	CryoEM structure of quinol dependent Nitric Oxide Reductase with BRIL
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	41.70 Å
rg_electron	40.90 Å
i0	487034000.00
molecular_weight	192250.0 kDa
excluded_volume	244820 Å³
envelope_volume	312680 Å³
shell_volume	63454 Å³
envelope_diameter	152.7 Å
shell_rg	46.14 Å
envelope_rg	41.45 Å
shape_rg	40.86 Å
total_rg	41.34 Å
total_atoms	13612
n_residues	1704
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	143.7 Å
rg_real	41.79 Å
rg_real_error	1.32 Å
i0_real	4.8700e+08
i0_real_error	9.5060e+06
rg_reciprocal	41.71 Å
i0_reciprocal	487000000.0000
total_estimate	0.8740
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	45.4 Å
skewness	0.408
kurtosis	-0.317
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	166300000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.905

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Nitric oxide reductase subunit B,Soluble cytochrome b562
formula_weight	94903.2 kDa
ec_number	1.7.2.5
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	13612

MGPYRRLWFTLIAVLAVTFALLGFYGGEVYRQAPPIPEEVASADGTRLFGRDDILDGQTAWQSIGGMQLGSIWGHGAYQAPDWTADWLHRELMAWLDLAARDAHGRDYGQLDAPAQAALREQLKAEYRANRADAAGGKLTLSPRRAQAVAQTEAYYDQLFSDAPALHRSRENYAMKENTLPDANRRRQMTHFFFWTAWAAATEREGTSVTYTNNWPHEPLIGNHPSSENVMWSIISVVVLLAGIGLLIWAWAFLRGKEEDEPPAPARDPLTTFALTPSQRALGKYLFLVVALFGFQVLLGGFTAHYTVEGQKFYGIDLSQWFPYSLVRTWHIQSALFWIATGFLAAGLFLAPLINGGRDPKYQKAGVDILFWALVLVVVGSFAGNYLAIAQIMPPDLNFWLGHQGYEYVDLGRLWQIGKFAGICFWLVLMLRGIVPALRTPGGDKNLLALLTASVGAIGLFYGAGFFYGERTHLTVMEYWRWWIVHLWVEGFFEVFATTALAFIFSTLGLVSRRMATTASLASASLFMLGGIPGTFHHLYFAGTTTPVMAVGASFSALEVVPLIVLGHEAWENWRLKTRAPWMENLKWPLMCFVAVAFWNMLGAGVFGFMINPPVSLYYIQGLNTTPVHAHAALFGVYGFLALGFTLLVLRYIRPQYALSPGLMKLAFWGLNLGLALMIFTSLLPIGLIQFHASVSEGMWYARSEAFMQQDILKTLRWGRTFGDVVFLLGALAMVVQVILGLLSGKADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYL

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	syn
entity_count	4

Entity 3 non-polymer

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

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

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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	3.40 Å
resolution_method	—
num_particles	100494

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