SAXSdb — 9pxf

▼

1. Structure Basics

entry_id	9pxf
deposition_date	2025-08-05
title	Ammonia monooxygenase in native membranes from N. briensis
keywords	ammonia oxidation, copper enzyme, membrane protein, active site, OXIDOREDUCTASE; OXIDOREDUCTASE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	43.62 Å
rg_electron	42.56 Å
i0	1232860000.00
molecular_weight	312920.0 kDa
excluded_volume	399440 Å³
envelope_volume	523130 Å³
shell_volume	95965 Å³
envelope_diameter	135.2 Å
shell_rg	52.78 Å
envelope_rg	41.68 Å
shape_rg	42.54 Å
total_rg	43.10 Å
total_atoms	22338
n_residues	2715
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

▼

3. P(r) Analysis (GNOM)

dmax	133.2 Å
rg_real	43.28 Å
rg_real_error	0.65 Å
i0_real	1.2330e+09
i0_real_error	2.0630e+07
rg_reciprocal	43.62 Å
i0_reciprocal	1233000000.0000
total_estimate	0.8809
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.2 Å
skewness	0.018
kurtosis	-0.450
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	223000000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.885

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Ammonia monooxygenase subunit C
formula_weight	29534.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,H,I
atom_count	23186

DMSEWYDSRWYKFGLITMLLVAIFWVWYQRTYAYSHGMDSMEPEFEKVWMGLWRVHMIVMPIFALITWGWIWKTRDTNLDNLDPKLEVKRYFYWMMWLGVYLFGVYWGGSFFTEQDASWHQVIIRDTSFTPSHVVVFYGSFPMYIVCGVASYLYAMTRLPLYSRGTSFPLVMAIAGPLMILPNVGLNEWGHAFWFMEELFSAPLHWGFVILGWSGLFAGGIAAQIITRYSNLTDVVWNGQSKVILNNRIVP

Source

organism	Nitrosospira briensis
ncbi_taxonomy_id	35799
host_organism	Nitrosospira briensis

Entity 2 polymer

description	Ammonia monooxygenase subunit A
formula_weight	31288.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

SRTDEILKAAKMPPEAVKMSRMIDAVYFPILCILLVGTYHMHFMLLAGDWDFWLDWKDRQWWPVVTPIVGITYCAAIMYYLWVNYRLPFGATLCIVCLLTGEWLTRFWGFYWWSHYPISFVFPSTMIPGALVMDTVMLLTRNWMITALVGGGAFGLLFYPGNWTIFGPTHLPLVAEGVLLSVADYTGFLYVRTGTPEYVRLIEQGSLRTFGGHTTVIASFFAAFVSMLMFCVWWYFGKLYCTAFFYVKGARGRVTMKNDVTAFGEEGFPEGIK

Source

organism	Nitrosospira briensis
ncbi_taxonomy_id	35799
host_organism	Nitrosospira briensis

Entity 3 polymer

description	Ammonia monooxygenase subunit B
formula_weight	42675.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C

HGERSQEPFLRMRTIQWYDMKWGPETTKVNDFASMTGKFHLAEDWPRAVGKPGRAFFNVGSPSPVFVRLSTKLNGEPTMISGPLEIGRDYAFEVKLKARIPGRHHMHAMVNIKDAGPIAGPAAWMNITGSWDDFTNPIKLLTGETIDTETFNFSNGIFWHALWMALGIFWIGYYVARPMFLPRSRVLLAYGDELLIDPMDKKVAWVVLILTLGIVWGGYRYTENKHPYTVPIQAGESKVAPLPVKPNPIAIKVTHANYDVPGRALRVTMMVTNSGDSAYRIGEFTTAGVRFINKVGLKHMDRGYPKELVATGLSFDNDTPIQPGETREVKMEAKDALWEVQRLMALLGDPESRFGGLLMTWNDAGDRNINSIAGAVIPVFT

Source

organism	Nitrosospira briensis
ncbi_taxonomy_id	35799
host_organism	Nitrosospira briensis

Entity 4 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	9

Entity 5 non-polymer

description	(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
formula_weight	763.1 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	848

▶

6. Citations (1)

▶

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	2.58 Å
resolution_method	—
num_particles	212075

fit	/app/data/saxs_computation/px/9pxf/9pxf.fit
pddf	/app/data/pr_computation/px/9pxf/9pxf.pr.out
profile	/app/data/saxs_computation/px/9pxf/9pxf.dat

Ammonia monooxygenase in native membranes from N. briensis

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)