SAXSdb — 9tox

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1. Structure Basics

entry_id	9tox
deposition_date	2025-12-17
last_revision	2026-06-03
title	CO dehydrogenase 2 variant A559W
keywords	CODH, channel, A559W, CLUSTER C, 4FE-4S, IRON, IRON-SULFUR, NICKEL, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

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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	24.98 Å
rg_electron	23.83 Å
i0	78111000.00
molecular_weight	67631.0 kDa
excluded_volume	84053 Å³
envelope_volume	96604 Å³
shell_volume	32462 Å³
envelope_diameter	79.4 Å
shell_rg	32.18 Å
envelope_rg	24.10 Å
shape_rg	23.83 Å
total_rg	24.67 Å
total_atoms	4684
n_residues	633
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	77.5 Å
rg_real	24.79 Å
rg_real_error	0.39 Å
i0_real	7.8110e+07
i0_real_error	1.0130e+06
rg_reciprocal	24.83 Å
i0_reciprocal	78110000.0000
total_estimate	0.9031
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	30.7 Å
skewness	0.114
kurtosis	-0.537
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	8811000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Carbon monoxide dehydrogenase 2
formula_weight	66776.1 kDa
ec_number	1.2.7.4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	X
atom_count	4959

QNLKSTDRAVQQMLDKAKREGIQTVWDRYEAMKPQCGFGETGLCCRHCLQGPCRINPFGDEPKVGICGATAEVIVARGLDRSIAAGAAGHSGHAKHLAHTLKKAVQGKAASYMIKDRTKLHSIAKRLGIPTEGQKDEDIALEVAKAALADFHEKDTPVLWVTTVLPPSRVKVLSAHGLIPAGIDHEIAEIMHRTSMGCDADAQNLLLGGLRCSLADLAGCYMGTDLADILFGTPAPVVTESNLGVLKADAVNVAVHGHNPVLSDIIVSVSKEMENEARAAGATGINVVGICCTGNEVLMRHGIPACTHSVSQEMAMITGALDAMILDYQCIQPSVATIAECTGTTVITTMEMSKITGATHVNFAEEAAVENAKQILRLAIDTFKRRKGKPVEIPNIKTKVVAGFSTEAIINALSKLNANDPLKPLIDNVVNGNIRGVCLFAGCNNVKVPQDQNFTTIARKLLKQNVLVVATGCGAGALMRHGFMDPANVDELCGDGLKAVLTAIGEANGLGGPLPPVLHMGSCVDNSRAVALVAALANRLGVDLDRLPVVASAAEWMHEKAVAIGTWAVTIGLPTHIGVLPPITGSLPVTQILTSSVKDITGGYFIVELDPETAADKLLAAINERRAGLGLPW

Source

organism	Carboxydothermus hydrogenoformans Z-2901
ncbi_taxonomy_id	246194
host_organism	Escherichia coli B

Entity 2 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	FE(3)-NI(1)-S(4) CLUSTER
formula_weight	354.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	182

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6. Citations (1)

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length_a	111.310 Å
length_b	75.330 Å
length_c	71.590 Å
angle_alpha	90.00 °
angle_beta	111.56 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.490 Å
resolution_low	40.799 Å
r_factor	—
r_work	0.1749
r_free	0.2126

fit	/app/data/saxs_computation/to/9tox/9tox.fit
pddf	/app/data/pr_computation/to/9tox/9tox.pr.out
profile	/app/data/saxs_computation/to/9tox/9tox.dat

CO dehydrogenase 2 variant A559W

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

Diffraction