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9s45

ClxA from Clostridium cavendishii in complex with 3-amino,4-hydroxybenzoic acid and its adenylate

Method: X-RAY DIFFRACTION D_max: 126.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s45
deposition_date	2025-07-25
last_revision	2026-03-18
title	ClxA from Clostridium cavendishii in complex with 3-amino,4-hydroxybenzoic acid and its adenylate
keywords	ATP, amide, ligase, closoxazole; LIGASE
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	38.54 Å
rg_electron	37.81 Å
i0	452311000.00
molecular_weight	178330.0 kDa
excluded_volume	225300 Å³
envelope_volume	288400 Å³
shell_volume	61518 Å³
envelope_diameter	134.2 Å
shell_rg	45.30 Å
envelope_rg	37.72 Å
shape_rg	37.80 Å
total_rg	38.30 Å
total_atoms	12526
n_residues	1593
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	126.2 Å
rg_real	38.44 Å
rg_real_error	0.91 Å
i0_real	4.5230e+08
i0_real_error	7.6530e+06
rg_reciprocal	38.51 Å
i0_reciprocal	452300000.0000
total_estimate	0.8930
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.2 Å
skewness	0.254
kurtosis	-0.427
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	166600000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.921

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Phenylacetate-CoA ligase
formula_weight	45089.9 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	13419

MDSNSQLITKLNSALQIATKANFYKDRLGNIEIKSLDDFSKLPLTTKEDLRKLKPMEALTVDIEDLFQYHESFGTTGEPVSTWLTEKDFNAYGDQLNEFGVNFKSTDIVLNRFPYAISVPAHIFTNAIHKKGACVIPVSKASAISPLKRVANLIYKLRPSILTGIPDELIKLNKVAKFMDISLKDLGCIRAICTAGEMLSEGRKAKLESIFGAKVYNYYGCTECGNMAASCDEGHLHISKDFYVEILDPVTLKPVKEGKGKIIVTTLNKEAFPMIRYDLGDIGEIKYEKCSCGNDRPVLIHHGREIDLIKTSKGTITFKELQEEIFKLPNSVVGDVFRVKIQNDEVIVECEADEELDNSNSNLNLPIEVKIKRFNHGEILNIDNLIEIKPIAKPKYVEYVD

Source

organism	Clostridium cavendishii
ncbi_taxonomy_id	349931
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 3-azanyl-4-oxidanyl-benzoate
formula_weight	482.3 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	3-amino-4-hydroxybenzoic acid
formula_weight	153.1 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	785

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6. Citations (1)

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length_a	73.209 Å
length_b	80.241 Å
length_c	82.742 Å
angle_alpha	89.97 °
angle_beta	84.29 °
angle_gamma	76.16 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.150 Å
resolution_low	57.260 Å
r_factor	—
r_work	0.2100
r_free	0.2700

fit	/app/data/saxs_computation/s4/9s45/9s45.fit
pddf	/app/data/pr_computation/s4/9s45/9s45.pr.out
profile	/app/data/saxs_computation/s4/9s45/9s45.dat