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9s3l

ClxA from Clostridium cavendishii (apo)

Method: X-RAY DIFFRACTION D_max: 126.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s3l
deposition_date	2025-07-24
title	ClxA from Clostridium cavendishii (apo)
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	38.25 Å
rg_electron	37.53 Å
i0	419300000.00
molecular_weight	172270.0 kDa
excluded_volume	217830 Å³
envelope_volume	279170 Å³
shell_volume	60335 Å³
envelope_diameter	133.5 Å
shell_rg	44.85 Å
envelope_rg	37.22 Å
shape_rg	37.52 Å
total_rg	38.02 Å
total_atoms	12120
n_residues	1594
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	126.3 Å
rg_real	38.13 Å
rg_real_error	1.21 Å
i0_real	4.1930e+08
i0_real_error	7.1080e+06
rg_reciprocal	38.21 Å
i0_reciprocal	419300000.0000
total_estimate	0.8177
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.2 Å
skewness	0.249
kurtosis	-0.428
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	120800000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	12198

MDSNSQLITKLNSALQIATKANFYKDRLGNIEIKSLDDFSKLPLTTKEDLRKLKPMEALTVDIEDLFQYHESFGTTGEPVSTWLTEKDFNAYGDQLNEFGVNFKSTDIVLNRFPYAISVPAHIFTNAIHKKGACVIPVSKASAISPLKRVANLIYKLRPSILTGIPDELIKLNKVAKFMDISLKDLGCIRAICTAGEMLSEGRKAKLESIFGAKVYNYYGCTECGNMAASCDEGHLHISKDFYVEILDPVTLKPVKEGKGKIIVTTLNKEAFPMIRYDLGDIGEIKYEKCSCGNDRPVLIHHGREIDLIKTSKGTITFKELQEEIFKLPNSVVGDVFRVKIQNDEVIVECEADEELDNSNSNLNLPIEVKIKRFNHGEILNIDNLIEIKPIAKPKYVEYVD

Source

organism	Clostridium cavendishii
ncbi_taxonomy_id	349931
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	78

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6. Citations (1)

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length_a	71.940 Å
length_b	79.970 Å
length_c	81.770 Å
angle_alpha	90.26 °
angle_beta	95.58 °
angle_gamma	103.50 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.570 Å
resolution_low	40.710 Å
r_factor	0.2669
r_work	0.2651
r_free	0.3009

fit	/app/data/saxs_computation/s3/9s3l/9s3l.fit
pddf	/app/data/pr_computation/s3/9s3l/9s3l.pr.out
profile	/app/data/saxs_computation/s3/9s3l/9s3l.dat

ClxA from Clostridium cavendishii (apo)

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